1
|
Tkalec KI, Hayes AJ, Lim KS, Lewis JM, Davies MR, Scott NE. Glycan-Tailored Glycoproteomic Analysis Reveals Serine is the Sole Residue Subjected to O-Linked Glycosylation in Acinetobacter baumannii. J Proteome Res 2024; 23:2474-2494. [PMID: 38850255 DOI: 10.1021/acs.jproteome.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein glycosylation is a ubiquitous process observed across all domains of life. Within the human pathogen Acinetobacter baumannii, O-linked glycosylation is required for virulence; however, the targets and conservation of glycosylation events remain poorly defined. In this work, we expand our understanding of the breadth and site specificity of glycosylation within A. baumannii by demonstrating the value of strain specific glycan electron-transfer/higher-energy collision dissociation (EThcD) triggering for bacterial glycoproteomics. By coupling tailored EThcD-triggering regimes to complementary glycopeptide enrichment approaches, we assessed the observable glycoproteome of three A. baumannii strains (ATCC19606, BAL062, and D1279779). Combining glycopeptide enrichment techniques including ion mobility (FAIMS), metal oxide affinity chromatography (titanium dioxide), and hydrophilic interaction liquid chromatography (ZIC-HILIC), as well as the use of multiple proteases (trypsin, GluC, pepsin, and thermolysis), we expand the known A. baumannii glycoproteome to 33 unique glycoproteins containing 42 glycosylation sites. We demonstrate that serine is the sole residue subjected to glycosylation with the substitution of serine for threonine abolishing glycosylation in model glycoproteins. An A. baumannii pan-genome built from 576 reference genomes identified that serine glycosylation sites are highly conserved. Combined this work expands our knowledge of the conservation and site specificity of A. baumannii O-linked glycosylation.
Collapse
Affiliation(s)
- Kristian I Tkalec
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Kataleen S Lim
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| |
Collapse
|
2
|
Lewis JM, Jebeli L, Coulon PML, Lay CE, Scott NE. Glycoproteomic and proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility. Microbiol Spectr 2024; 12:e0034624. [PMID: 38709084 DOI: 10.1128/spectrum.00346-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Across the Burkholderia genus O-linked protein glycosylation is highly conserved. While the inhibition of glycosylation has been shown to be detrimental for virulence in Burkholderia cepacia complex species, such as Burkholderia cenocepacia, little is known about how specific glycosylation sites impact protein functionality. Within this study, we sought to improve our understanding of the breadth, dynamics, and requirement for glycosylation across the B. cenocepacia O-glycoproteome. Assessing the B. cenocepacia glycoproteome across different culture media using complementary glycoproteomic approaches, we increase the known glycoproteome to 141 glycoproteins. Leveraging this repertoire of glycoproteins, we quantitively assessed the glycoproteome of B. cenocepacia using Data-Independent Acquisition (DIA) revealing the B. cenocepacia glycoproteome is largely stable across conditions with most glycoproteins constitutively expressed. Examination of how the absence of glycosylation impacts the glycoproteome reveals that the protein abundance of only five glycoproteins (BCAL1086, BCAL2974, BCAL0525, BCAM0505, and BCAL0127) are altered by the loss of glycosylation. Assessing ΔfliF (ΔBCAL0525), ΔmotB (ΔBCAL0127), and ΔBCAM0505 strains, we demonstrate the loss of FliF, and to a lesser extent MotB, mirror the proteomic effects observed in the absence of glycosylation in ΔpglL. While both MotB and FliF are essential for motility, we find loss of glycosylation sites in MotB or FliF does not impact motility supporting these sites are dispensable for function. Combined this work broadens our understanding of the B. cenocepacia glycoproteome supporting that the loss of glycoproteins in the absence of glycosylation is not an indicator of the requirement for glycosylation for protein function. IMPORTANCE Burkholderia cenocepacia is an opportunistic pathogen of concern within the Cystic Fibrosis community. Despite a greater appreciation of the unique physiology of B. cenocepacia gained over the last 20 years a complete understanding of the proteome and especially the O-glycoproteome, is lacking. In this study, we utilize systems biology approaches to expand the known B. cenocepacia glycoproteome as well as track the dynamics of glycoproteins across growth phases, culturing media and in response to the loss of glycosylation. We show that the glycoproteome of B. cenocepacia is largely stable across conditions and that the loss of glycosylation only impacts five glycoproteins including the motility associated proteins FliF and MotB. Examination of MotB and FliF shows, while these proteins are essential for motility, glycosylation is dispensable. Combined this work supports that B. cenocepacia glycosylation can be dispensable for protein function and may influence protein properties beyond stability.
Collapse
Affiliation(s)
- Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Pauline M L Coulon
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Catrina E Lay
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| |
Collapse
|
3
|
Yang Y, Tan L, He S, Hao B, Huang X, Zhou Y, Shang W, Peng H, Hu Z, Ding R, Rao X. Sub-MIC vancomycin enhances the antibiotic tolerance of vancomycin-intermediate Staphylococcus aureus through downregulation of protein succinylation. Microbiol Res 2024; 282:127635. [PMID: 38340572 DOI: 10.1016/j.micres.2024.127635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Bacteria develop tolerance after transient exposure to antibiotics, and tolerance is a significant driver of resistance. The purpose of this study is to evaluate the mechanisms underlying tolerance formation in vancomycin-intermediate Staphylococcus aureus (VISA) strains. VISA strains were cultured with sub-minimum inhibitory concentrations (sub-MICs) of vancomycin. Enhanced vancomycin tolerance was observed in VISA strains with distinct genetic lineages. Western blot revealed that the VISA protein succinylation (Ksucc) levels decreased with the increase in vancomycin exposure. Importantly, Ksucc modification, vancomycin tolerance, and cell wall synthesis were simultaneously affected after deletion of SacobB, which encodes a desuccinylase in S. aureus. Several Ksucc sites were identified in MurA, and vancomycin MIC levels of murA mutant and Ksucc-simulated (MurA(K69E) and MurA(K191E)) mutants were reduced. The vancomycin MIC levels of K65-MurA(K191E) in particular decreased to 1 mg/L, converting VISA strain K65 to a vancomycin-susceptible S. aureus strain. We further demonstrated that the enzymatic activity of MurA was dependent on Ksucc modification. Our data suggested the influence of vancomycin exposure on bacterial tolerance, and protein Ksucc modification is a novel mechanism in regulating vancomycin tolerance.
Collapse
Affiliation(s)
- Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Li Tan
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Siyuan He
- College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Bo Hao
- College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiaonan Huang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yumin Zhou
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Ruolan Ding
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing 400044, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China.
| |
Collapse
|
4
|
Man L, Soh PXY, McEnearney TE, Cain JA, Dale AL, Cordwell SJ. Multi-Omics of Campylobacter jejuni Growth in Chicken Exudate Reveals Molecular Remodelling Associated with Altered Virulence and Survival Phenotypes. Microorganisms 2024; 12:860. [PMID: 38792690 PMCID: PMC11123243 DOI: 10.3390/microorganisms12050860] [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: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Campylobacter jejuni is the leading cause of foodborne human gastroenteritis in the developed world. Infections are largely acquired from poultry produced for human consumption and poor food handling is thus a major risk factor. Chicken exudate (CE) is a liquid produced from defrosted commercial chicken products that facilitates C. jejuni growth. We examined the response of C. jejuni to growth in CE using a multi-omics approach. Changes in the C. jejuni proteome were assessed by label-based liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We quantified 1328 and 1304 proteins, respectively, in experiments comparing 5% CE in Mueller-Hinton (MH) medium and 100% CE with MH-only controls. These proteins represent 81.8% and 80.3% of the predicted C. jejuni NCTC11168 proteome. Growth in CE induced profound remodelling of the proteome. These changes were typically conserved between 5% and 100% CE, with a greater magnitude of change observed in 100% CE. We confirmed that CE induced C. jejuni biofilm formation, as well as increasing motility and resistance against oxidative stress, consistent with changes to proteins representing those functions. Assessment of the C. jejuni metabolome showed CE also led to increased intracellular abundances of serine, proline, and lactate that were correlated with the elevated abundances of their respective transporters. Analysis of carbon source uptake showed prolonged culture supernatant retention of proline and succinate in CE-supplemented medium. Metabolomics data provided preliminary evidence for the uptake of chicken-meat-associated dipeptides. C. jejuni exposed to CE showed increased resistance to several antibiotics, including polymyxin B, consistent with changes to tripartite efflux system proteins and those involved in the synthesis of lipid A. The C. jejuni CE proteome was also characterised by very large increases in proteins associated with iron acquisition, while a decrease in proteins containing iron-sulphur clusters was also observed. Our data suggest CE is both oxygen- and iron-limiting and provide evidence of factors required for phenotypic remodelling to enable C. jejuni survival on poultry products.
Collapse
Affiliation(s)
- Lok Man
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pamela X. Y. Soh
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tess E. McEnearney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joel A. Cain
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ashleigh L. Dale
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stuart J. Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
5
|
Dang J, Shu J, Wang R, Yu H, Chen Z, Yan W, Zhao B, Ding L, Wang Y, Hu H, Li Z. The glycopatterns of Pseudomonas aeruginosa as a potential biomarker for its carbapenem resistance. Microbiol Spectr 2023; 11:e0200123. [PMID: 37861315 PMCID: PMC10714932 DOI: 10.1128/spectrum.02001-23] [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: 05/23/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Bacterial surface glycans are an attractive therapeutic target in response to antibiotics; however, current knowledge of the corresponding mechanisms is rather limited. Antimicrobial susceptibility testing, genome sequencing, and MALDI-TOF MS, commonly used in recent years to analyze bacterial resistance, are unable to rapidly and efficiently establish associations between glycans and resistance. The discovery of new antimicrobial strategies still requires the introduction of promising analytical methods. In this study, we applied lectin microarray technology and a machine-learning model to screen for important glycan structures associated with carbapenem-resistant P. aeruginosa. This work highlights that specific glycopatterns can be important biomarkers associated with bacterial antibiotic resistance, which promises to provide a rapid entry point for exploring new resistance mechanisms in pathogens.
Collapse
Affiliation(s)
- Jing Dang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jian Shu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Ruiying Wang
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Hanjie Yu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Wenbo Yan
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Bingxiang Zhao
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Li Ding
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yuzi Wang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Huizheng Hu
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Zheng Li
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| |
Collapse
|
6
|
Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [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: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
Collapse
Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
| |
Collapse
|
7
|
Lin AD, Fischer JDSDG, Santos MDM, Camillo-Andrade AC, Kurt LU, Souza TACB, Lajas ABL, Rivera B, Portela M, Duran R, Mira MT, Pillonetto M, Carvalho PC. Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals. J Proteomics 2023; 289:105012. [PMID: 37748533 DOI: 10.1016/j.jprot.2023.105012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SIGNIFICANCE: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.
Collapse
Affiliation(s)
- Amanda Dal Lin
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil
| | - Juliana de S da G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Amanda Caroline Camillo-Andrade
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Louise Ulrich Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Tatiana A C B Souza
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Ana Beatriz Lyrio Lajas
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Bernardina Rivera
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Rosario Duran
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Marcelo Távora Mira
- Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil
| | - Marcelo Pillonetto
- Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil; Laboratório Central do Estado do Paraná, Brazil.
| | - Paulo Costa Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil.
| |
Collapse
|
8
|
Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
Collapse
Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
| |
Collapse
|
9
|
Lewis J, Scott NE. CRISPRi-Mediated Silencing of Burkholderia O-Linked Glycosylation Systems Enables the Depletion of Glycosylation Yet Results in Modest Proteome Impacts. J Proteome Res 2023; 22:1762-1778. [PMID: 36995114 PMCID: PMC10243306 DOI: 10.1021/acs.jproteome.2c00790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Indexed: 03/31/2023]
Abstract
The process of O-linked protein glycosylation is highly conserved across the Burkholderia genus and mediated by the oligosaccharyltransferase PglL. While our understanding of Burkholderia glycoproteomes has increased in recent years, little is known about how Burkholderia species respond to modulations in glycosylation. Utilizing CRISPR interference (CRISPRi), we explored the impact of silencing of O-linked glycosylation across four species of Burkholderia; Burkholderia cenocepacia K56-2, Burkholderia diffusa MSMB375, Burkholderia multivorans ATCC17616, and Burkholderia thailandensis E264. Proteomic and glycoproteomic analyses revealed that while CRISPRi enabled inducible silencing of PglL, this did not abolish glycosylation, nor recapitulate phenotypes such as proteome changes or alterations in motility that are associated with glycosylation null strains, despite inhibition of glycosylation by nearly 90%. Importantly, this work also demonstrated that CRISPRi induction with high levels of rhamnose leads to extensive impacts on the Burkholderia proteomes, which without appropriate controls mask the impacts specifically driven by CRISPRi guides. Combined, this work revealed that while CRISPRi allows the modulation of O-linked glycosylation with reductions up to 90% at a phenotypic and proteome levels, Burkholderia appears to demonstrate a robust tolerance to fluctuations in glycosylation capacity.
Collapse
Affiliation(s)
- Jessica
M. Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute
for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute
for Infection and Immunity, Melbourne 3000, Australia
| |
Collapse
|
10
|
Newman KE, Khalid S. Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS Comput Biol 2023; 19:e1010841. [PMID: 36638139 PMCID: PMC9879487 DOI: 10.1371/journal.pcbi.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/26/2023] [Accepted: 12/26/2022] [Indexed: 01/14/2023] Open
Abstract
The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the protein is N-glycosylated, with the glycans playing a key role in the effective function of this system. In this work we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid and a macrolide antibiotic. These, and additional equilibrium simulations suggest that the anionic bile acid utilises multivalent cations to climb the ladder of acidic residues that line the interior surface of the protein.
Collapse
Affiliation(s)
- Kahlan E. Newman
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
11
|
McDonald JB, Scott NE, Underwood GJ, Andrews DM, Van TTH, Moore RJ. Characterisation of N-linked protein glycosylation in the bacterial pathogen Campylobacter hepaticus. Sci Rep 2023; 13:227. [PMID: 36604449 PMCID: PMC9816155 DOI: 10.1038/s41598-022-26532-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Campylobacter hepaticus is an important pathogen which causes Spotty Liver Disease (SLD) in layer chickens. SLD results in an increase in mortality and a significant decrease in egg production and therefore is an important economic concern of the global poultry industry. The human pathogen Campylobacter jejuni encodes an N-linked glycosylation system that plays fundamental roles in host colonization and pathogenicity. While N-linked glycosylation has been extensively studied in C. jejuni and is now known to occur in a range of Campylobacter species, little is known about C. hepaticus glycosylation. In this study glycoproteomic analysis was used to confirm the functionality of the C. hepaticus N-glycosylation system. It was shown that C. hepaticus HV10T modifies > 35 proteins with an N-linked heptasaccharide glycan. C. hepaticus shares highly conserved glycoproteins with C. jejuni that are involved in host colonisation and also possesses unique glycoproteins which may contribute to its ability to survive in challenging host environments. C. hepaticus N-glycosylation may function as an important virulence factor, providing an opportunity to investigate and develop a better understanding the system's role in poultry infection.
Collapse
Affiliation(s)
- Jamieson B McDonald
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Greg J Underwood
- Bioproperties Pty Ltd, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Daniel M Andrews
- Bioproperties Pty Ltd, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia.
| |
Collapse
|
12
|
Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
Collapse
Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| |
Collapse
|
13
|
dos Reis JS, Rodrigues da Costa Santos MA, Mendonça DP, Martins do Nascimento SI, Barcelos PM, Correia de Lima RG, da Costa KM, Freire-de-Lima CG, Morrot A, Previato JO, Mendonça Previato L, da Fonseca LM, Freire-de-Lima L. Glycobiology of Cancer: Sugar Drives the Show. MEDICINES 2022; 9:medicines9060034. [PMID: 35736247 PMCID: PMC9229842 DOI: 10.3390/medicines9060034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
Cancer development and progression is associated with aberrant changes in cellular glycosylation. Cells expressing altered glycan-structures are recognized by cells of the immune system, favoring the induction of inhibitory immune processes which subsequently promote tumor growth and spreading. Here, we discuss about the importance of glycobiology in modern medicine, taking into account the impact of altered glycan structures expressed in cancer cells as potential glycobiomarkers of disease, as well as on cancer development and progression.
Collapse
Affiliation(s)
- Jhenifer Santos dos Reis
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Marcos André Rodrigues da Costa Santos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Daniella Pereira Mendonça
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Stefani Ingrid Martins do Nascimento
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Pedro Marçal Barcelos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Rafaela Gomes Correia de Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Kelli Monteiro da Costa
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Alexandre Morrot
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil;
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21044-020, Brazil
| | - Jose Osvaldo Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Lucia Mendonça Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
- Correspondence: ; Tel./Fax: +55-21-3938-6646
| |
Collapse
|
14
|
Cain JA, Dale AL, Cordwell SJ. Exploiting pglB Oligosaccharyltransferase-Positive and -Negative Campylobacter jejuni and a Multiprotease Digestion Strategy to Identify Novel Sites Modified by N-Linked Protein Glycosylation. J Proteome Res 2021; 20:4995-5009. [PMID: 34677046 DOI: 10.1021/acs.jproteome.1c00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is a bacterial pathogen encoding a unique N-linked glycosylation (pgl) system that mediates attachment of a heptasaccharide to N-sequon-containing membrane proteins by the PglB oligosaccharyltransferase (OST). Many targets of PglB are known, yet only a fraction of sequons are experimentally confirmed, and site occupancy remains elusive. We exploited pglB-positive (wild-type; WT) and -negative (ΔpglB) proteomes to identify potential glycosites. The nonglycosylated forms of known glycopeptides were typically increased in protein normalized abundance in ΔpglB relative to WT and restored by pglB reintroduction (ΔpglB::pglB). Sequon-containing peptide abundances were thus consistent with significant site occupancy in the presence of the OST. Peptides with novel sequons were either unaltered (likely not glycosylated) or showed abundance consistent with known glycopeptides. Topology analysis revealed that unaltered sequons often displayed cytoplasmic localization, despite originating from membrane proteins. Novel glycosites were confirmed using parallel multiprotease digestion, LC-MS/MS, and FAIMS-MS to define the glycoproteomes of WT and ΔpglB::pglB C. jejuni. We identified 142 glycosites, of which 32 were novel, and 83% of sites predicted by proteomics were validated. There are now 166 experimentally verified C. jejuni glycosites and evidence for occupancy or nonoccupancy of 31 additional sites. This study serves as a model for the use of OST-negative cells and proteomics for highlighting novel glycosites and determining occupancy in a range of organisms.
Collapse
Affiliation(s)
- Joel A Cain
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Ashleigh L Dale
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney 2006, Australia
| |
Collapse
|
15
|
N-glycosylation of a cargo protein C-terminal domain recognized by the type IX secretion system in Cytophaga hutchinsonii affects protein secretion and localization. Appl Environ Microbiol 2021; 88:e0160621. [PMID: 34644163 DOI: 10.1128/aem.01606-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytophaga hutchinsonii is a Gram-negative bacterium belonging to the phylum Bacteroidetes. It digests crystalline cellulose with an unknown mechanism, and possesses a type IX secretion system (T9SS) that can recognize the C-terminal domain (CTD) of the cargo protein as a signal. In this study, the functions of CTD in the secretion and localization of T9SS substrates in C. hutchinsonii were studied by fusing the green fluorescent protein (GFP) with CTD from CHU_2708. CTD is necessary for the secretion of GFP by C. hutchinsonii T9SS. The GFP-CTDCHU_2708 fusion protein was found to be glycosylated in the periplasm with a molecular mass about 5 kDa higher than that predicted from its sequence. The glycosylated protein was sensitive to peptide-N-glycosidase F which can hydrolyze N-linked oligosaccharides. Analyses of mutants obtained by site-directed mutagenesis of asparagine residues in the N-X-S/T motif of CTDCHU_2708 suggest that N-glycosylation occurred on the CTD. CTD N-glycosylation is important for the secretion and localization of GFP-CTD recombinant proteins in C. hutchinsonii. Glycosyltransferase encoding gene chu_3842, a homologous gene of Campylobacter jejuni pglA, was found to participate in the N-glycosylation of C. hutchinsonii. Deletion of chu_3842 affected cell motility, cellulose degradation, and cell resistance to some chemicals. Our study provided the evidence that CTD as the signal of T9SS was N-glycosylated in the periplasm of C. hutchinsonii. IMPORTANCE The bacterial N-glycosylation system has previously only been found in several species of Proteobacteria and Campylobacterota, and the role of N-linked glycans in bacteria is still not fully understood. C. hutchinsonii has a unique cell-contact cellulose degradation mechanism, and many cell surface proteins including cellulases are secreted by the T9SS. Here, we found that C. hutchinsonii, a member of the phylum Bacteroidetes, has an N-glycosylation system. Glycosyltransferase CHU_3842 was found to participate in the N-glycosylation of C. hutchinsonii proteins, and had effects on cell resistance to some chemicals, cell motility, and cellulose degradation. Moreover, N-glycosylation occurs on the CTD translocation signal of T9SS. The glycosylation of CTD apears to play an important role in affecting T9SS substrates transportation and localization. This study enriched our understanding of the widespread existence and multiple biological roles of N-glycosylation in bacteria.
Collapse
|
16
|
Yakovlieva L, Fülleborn JA, Walvoort MTC. Opportunities and Challenges of Bacterial Glycosylation for the Development of Novel Antibacterial Strategies. Front Microbiol 2021; 12:745702. [PMID: 34630370 PMCID: PMC8498110 DOI: 10.3389/fmicb.2021.745702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
Glycosylation is a ubiquitous process that is universally conserved in nature. The various products of glycosylation, such as polysaccharides, glycoproteins, and glycolipids, perform a myriad of intra- and extracellular functions. The multitude of roles performed by these molecules is reflected in the significant diversity of glycan structures and linkages found in eukaryotes and prokaryotes. Importantly, glycosylation is highly relevant for the virulence of many bacterial pathogens. Various surface-associated glycoconjugates have been identified in bacteria that promote infectious behavior and survival in the host through motility, adhesion, molecular mimicry, and immune system manipulation. Interestingly, bacterial glycosylation systems that produce these virulence factors frequently feature rare monosaccharides and unusual glycosylation mechanisms. Owing to their marked difference from human glycosylation, bacterial glycosylation systems constitute promising antibacterial targets. With the rise of antibiotic resistance and depletion of the antibiotic pipeline, novel drug targets are urgently needed. Bacteria-specific glycosylation systems are especially promising for antivirulence therapies that do not eliminate a bacterial population, but rather alleviate its pathogenesis. In this review, we describe a selection of unique glycosylation systems in bacterial pathogens and their role in bacterial homeostasis and infection, with a focus on virulence factors. In addition, recent advances to inhibit the enzymes involved in these glycosylation systems and target the bacterial glycan structures directly will be highlighted. Together, this review provides an overview of the current status and promise for the future of using bacterial glycosylation to develop novel antibacterial strategies.
Collapse
Affiliation(s)
- Liubov Yakovlieva
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Julius A Fülleborn
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Marthe T C Walvoort
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| |
Collapse
|
17
|
Mauri M, Sannasiddappa TH, Vohra P, Corona-Torres R, Smith AA, Chintoan-Uta C, Bremner A, Terra VS, Abouelhadid S, Stevens MP, Grant AJ, Cuccui J, Wren BW. Multivalent poultry vaccine development using Protein Glycan Coupling Technology. Microb Cell Fact 2021; 20:193. [PMID: 34600535 PMCID: PMC8487346 DOI: 10.1186/s12934-021-01682-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Poultry is the world's most popular animal-based food and global production has tripled in the past 20 years alone. Low-cost vaccines that can be combined to protect poultry against multiple infections are a current global imperative. Glycoconjugate vaccines, which consist of an immunogenic protein covalently coupled to glycan antigens of the targeted pathogen, have a proven track record in human vaccinology, but have yet to be used for livestock due to prohibitively high manufacturing costs. To overcome this, we use Protein Glycan Coupling Technology (PGCT), which enables the production of glycoconjugates in bacterial cells at considerably reduced costs, to generate a candidate glycan-based live vaccine intended to simultaneously protect against Campylobacter jejuni, avian pathogenic Escherichia coli (APEC) and Clostridium perfringens. Campylobacter is the most common cause of food poisoning, whereas colibacillosis and necrotic enteritis are widespread and devastating infectious diseases in poultry. RESULTS We demonstrate the functional transfer of C. jejuni protein glycosylation (pgl) locus into the genome of APEC χ7122 serotype O78:H9. The integration caused mild attenuation of the χ7122 strain following oral inoculation of chickens without impairing its ability to colonise the respiratory tract. We exploit the χ7122 pgl integrant as bacterial vectors delivering a glycoprotein decorated with the C. jejuni heptasaccharide glycan antigen. To this end we engineered χ7122 pgl to express glycosylated NetB toxoid from C. perfringens and tested its ability to reduce caecal colonisation of chickens by C. jejuni and protect against intra-air sac challenge with the homologous APEC strain. CONCLUSIONS We generated a candidate glycan-based multivalent live vaccine with the potential to induce protection against key avian and zoonotic pathogens (C. jejuni, APEC, C. perfringens). The live vaccine failed to significantly reduce Campylobacter colonisation under the conditions tested but was protective against homologous APEC challenge. Nevertheless, we present a strategy towards the production of low-cost "live-attenuated multivalent vaccine factories" with the ability to express glycoconjugates in poultry.
Collapse
Affiliation(s)
- Marta Mauri
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Thippeswamy H Sannasiddappa
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Prerna Vohra
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Ricardo Corona-Torres
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Alexander A Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Cosmin Chintoan-Uta
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Abi Bremner
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Vanessa S Terra
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sherif Abouelhadid
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Mark P Stevens
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK.
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK.
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| |
Collapse
|
18
|
Hayes AJ, Lewis JM, Davies MR, Scott NE. Burkholderia PglL enzymes are Serine preferring oligosaccharyltransferases which target conserved proteins across the Burkholderia genus. Commun Biol 2021; 4:1045. [PMID: 34493791 PMCID: PMC8423747 DOI: 10.1038/s42003-021-02588-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Glycosylation is increasingly recognised as a common protein modification within bacterial proteomes. While great strides have been made in identifying species that contain glycosylation systems, our understanding of the proteins and sites targeted by these systems is far more limited. Within this work we explore the conservation of glycoproteins and glycosylation sites across the pan-Burkholderia glycoproteome. Using a multi-protease glycoproteomic approach, we generate high-confidence glycoproteomes in two widely utilized B. cenocepacia strains, K56-2 and H111. This resource reveals glycosylation occurs exclusively at Serine residues and that glycoproteins/glycosylation sites are highly conserved across B. cenocepacia isolates. This preference for glycosylation at Serine residues is observed across at least 9 Burkholderia glycoproteomes, supporting that Serine is the dominant residue targeted by PglL-mediated glycosylation across the Burkholderia genus. Combined, this work demonstrates that PglL enzymes of the Burkholderia genus are Serine-preferring oligosaccharyltransferases that target conserved and shared protein substrates. Hayes et al provide a glycosylation site focused analysis of the glycoproteome of two widely utilized B. cenocepacia strains, K56-2 and H111. This team demonstrates that within these glycoproteomes Serine is the sole residue targeted for protein glycosylation and that glycoproteins/glycosylation sites are highly conserved across B. cenocepacia isolates.
Collapse
Affiliation(s)
- Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| |
Collapse
|
19
|
Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
Collapse
|
20
|
Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
Collapse
Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
| |
Collapse
|
21
|
Du Toit A. Aiming at the sweet spot of resistance. Nat Rev Microbiol 2021; 19:74-75. [PMID: 33262530 DOI: 10.1038/s41579-020-00494-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Elmi A, Nasher F, Dorrell N, Wren B, Gundogdu O. Revisiting Campylobacter jejuni Virulence and Fitness Factors: Role in Sensing, Adapting, and Competing. Front Cell Infect Microbiol 2021; 10:607704. [PMID: 33614526 PMCID: PMC7887314 DOI: 10.3389/fcimb.2020.607704] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
Campylobacter jejuni is the leading cause of bacterial foodborne gastroenteritis world wide and represents a major public health concern. Over the past two decades, significant progress in functional genomics, proteomics, enzymatic-based virulence profiling (EBVP), and the cellular biology of C. jejuni have improved our basic understanding of this important pathogen. We review key advances in our understanding of the multitude of emerging virulence factors that influence the outcome of C. jejuni–mediated infections. We highlight, the spatial and temporal dynamics of factors that promote C. jejuni to sense, adapt and survive in multiple hosts. Finally, we propose cohesive research directions to obtain a comprehensive understanding of C. jejuni virulence mechanisms.
Collapse
Affiliation(s)
- Abdi Elmi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fauzy Nasher
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nick Dorrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| |
Collapse
|