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Lushington GH, Linde A, Melgarejo T. Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog. BIOTECH 2023; 12:61. [PMID: 37987478 PMCID: PMC10660736 DOI: 10.3390/biotech12040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.
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Affiliation(s)
| | - Annika Linde
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
| | - Tonatiuh Melgarejo
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
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2
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Salivary peptidome analysis and protease prediction during orthodontic treatment with fixed appliances. Sci Rep 2023; 13:677. [PMID: 36635354 PMCID: PMC9837200 DOI: 10.1038/s41598-022-26969-3] [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: 10/05/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Orthodontic tooth movement (OTM) occurs through proteolytic remodelling within the periodontium following the application of external force to the tooth. This study describes the first characterization of the salivary peptidome and protease profile during the alignment stage of fixed appliance orthodontic treatment. Unstimulated whole mouth saliva from 16 orthodontic patients (10 males, 6 females, mean (SD) age 15.2 (1.6) years) was collected prior to fixed appliance placement (T1), 1-h (T2), 1-week (T3) following fixed appliance placement and on completion of mandibular arch alignment (T4). Salivary peptides were extracted using filtration followed by mass spectrometry to identify amino acid sequences. Protease prediction was carried out in silico using Proteasix and validated with gelatin zymography and enzyme-linked immunosorbent assay. A total of 2852 naturally-occurring peptides were detected, originating from 436 different proteins. Both collagen and statherin-derived peptide levels were increased at T2. Proteasix predicted 73 proteases potentially involved in generating these peptides, including metalloproteinases, calpains and cathepsins. Changes in predicted activity of proteases over time were also observed, with most metalloproteinases showing increased predicted activity at T2-T3. Increased gelatinolytic activity and MMP8/MMP9 levels were detected at T3. Collectively, multiple protein targets and changes in protease-predicted activity during OTM have been identified.
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3
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Torres-Maravilla E, Holowacz S, Delannoy J, Lenoir L, Jacouton E, Gervason S, Meynier M, Boucard AS, Carvalho FA, Barbut F, Bermúdez-Humarán LG, Langella P, Waligora-Dupriet AJ. Serpin-positive Bifidobacterium breve CNCM I-5644 improves intestinal permeability in two models of irritable bowel syndrome. Sci Rep 2022; 12:19776. [PMID: 36396717 PMCID: PMC9672316 DOI: 10.1038/s41598-022-21746-8] [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: 05/24/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Probiotic supplementation can help to mitigate the pathogenesis of irritable bowel syndrome (IBS) by reinforcing the intestinal barrier, and reducing both inflammation and proteolytic activity. Here, a combination of in vitro tests was performed on 33 Bifidobacterium strains as probiotic candidates for IBS. In addition to the classical tests performed, the detection of the serine protease inhibitor (serpin) enzyme capable of decreasing the high proteolytic activity found in IBS patients was included. Three serpin-positive strains were selected: Bifidobacterium breve CNCM I-5644, Bifidobacterium longum subsp. infantis CNCM I-5645 and B. longum CNCM I-5646 for their immunomodulation properties and protection of intestinal epithelial integrity in vitro. Furthermore, we found that B. breve CNCM I-5644 strain prevented intestinal hyperpermeability by upregulating Cingulin and Tight Junction Protein 1 mRNA levels and reducing pro-inflammatory markers. The ability of CNCM I-5644 strain to restore intestinal hyperpermeability (FITC-dextran) was shown in the murine model of low-grade inflammation induced by dinitrobenzene sulfonic acid (DNBS). This effect of this strain was corroborated in a second model of IBS, the neonatal maternal separation model in mice. Altogether, these data suggest that serpin-positive B. breve CNCM I-5644 may partially prevent disorders associated with increased barrier permeability such as IBS.
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Affiliation(s)
- Edgar Torres-Maravilla
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France ,grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France
| | - Sophie Holowacz
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Johanne Delannoy
- grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France
| | - Loïc Lenoir
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Elsa Jacouton
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Sandie Gervason
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Maëva Meynier
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Anne-Sophie Boucard
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Frédéric A. Carvalho
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Frédéric Barbut
- grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France ,grid.50550.350000 0001 2175 4109National Reference Laboratory for C. Difficile, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, 75012 Paris, France
| | - Luis G. Bermúdez-Humarán
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Philippe Langella
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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4
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Ménard S, Lacroix-Lamandé S, Ehrhardt K, Yan J, Grassl GA, Wiedemann A. Cross-Talk Between the Intestinal Epithelium and Salmonella Typhimurium. Front Microbiol 2022; 13:906238. [PMID: 35733975 PMCID: PMC9207452 DOI: 10.3389/fmicb.2022.906238] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovars are invasive gram-negative bacteria, causing a wide range of diseases from gastroenteritis to typhoid fever, representing a public health threat around the world. Salmonella gains access to the intestinal lumen after oral ingestion of contaminated food or water. The crucial initial step to establish infection is the interaction with the intestinal epithelium. Human-adapted serovars such as S. Typhi or S. Paratyphi disseminate to systemic organs and induce life-threatening disease known as typhoid fever, whereas broad-host serovars such as S. Typhimurium usually are limited to the intestine and responsible for gastroenteritis in humans. To overcome intestinal epithelial barrier, Salmonella developed mechanisms to induce cellular invasion, intracellular replication and to face host defence mechanisms. Depending on the serovar and the respective host organism, disease symptoms differ and are linked to the ability of the bacteria to manipulate the epithelial barrier for its own profit and cross the intestinal epithelium.This review will focus on S. Typhimurium (STm). To better understand STm pathogenesis, it is crucial to characterize the crosstalk between STm and the intestinal epithelium and decipher the mechanisms and epithelial cell types involved. Thus, the purpose of this review is to summarize our current knowledge on the molecular dialogue between STm and the various cell types constituting the intestinal epithelium with a focus on the mechanisms developed by STm to cross the intestinal epithelium and access to subepithelial or systemic sites and survive host defense mechanisms.
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Affiliation(s)
- Sandrine Ménard
- IRSD - Institut de Recherche en Santé Digestive, Université́ de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | | | - Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Jin Yan
- IRSD - Institut de Recherche en Santé Digestive, Université́ de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, China
- Research Center of Digestive Disease, Central South University, Changsha, China
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Agnès Wiedemann
- IRSD - Institut de Recherche en Santé Digestive, Université́ de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
- *Correspondence: Agnès Wiedemann,
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Giliazeva AG, Misheeva PS, Sharipova MR, Mardanova AM. Bioinformatic Analysis of a Grimelysin-like Protease in the Klebsiella oxytoca Strain NK-1. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-021-00924-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Dhakal P, Spencer TE. Generation and analysis of Prss28 and Prss29 deficient mice using CRISPR-Cas9 genome-editing. Mol Reprod Dev 2021; 88:482-489. [PMID: 33973295 PMCID: PMC8530251 DOI: 10.1002/mrd.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022]
Abstract
Glands of the uterus are essential for the establishment of pregnancy in mice and their products regulate embryo implantation and stromal cell decidualization critical for pregnancy establishment. Forkhead box A2 (FOXA2) is expressed specifically in the glands and a critical regulator of their differentiation, development and function. Progesterone and FOXA2 regulate members of a serine proteinase gene family (Prss28 and Prss29). Here, CRISPR-Cas9 genome-editing was used to create mice with a heterozygous or homozygous deletion of Prss28 or/and Prss29 to determine their biological roles in uterine function. Female mice lacking Prss28 and Prss29 or both developed normally and were fertile without alterations in uterine histoarchitecture, uterine gland number, or and gene expression. Thus, Prss28 and Prss29 are dispensable for female fertility and do not impact endometrial gland development or uterine function mice.
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Affiliation(s)
- Pramod Dhakal
- Division of Animal Sciences, Gynecology and Women’s Health, University of Missouri, Columbia, MO, USA
| | - Thomas E. Spencer
- Division of Animal Sciences, Gynecology and Women’s Health, University of Missouri, Columbia, MO, USA
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, MO, USA
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7
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Schoina C, Rodenburg SYA, Meijer HJG, Seidl MF, Lacambra LT, Bouwmeester K, Govers F. Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans. MOLECULAR PLANT PATHOLOGY 2021; 22:551-563. [PMID: 33657266 PMCID: PMC8035641 DOI: 10.1111/mpp.13043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Pathogens deploy a wide range of pathogenicity factors, including a plethora of proteases, to modify host tissue or manipulate host defences. Metalloproteases (MPs) have been implicated in virulence in several animal and plant pathogens. Here we investigated the repertoire of MPs in 46 stramenopile species including 37 oomycetes, 5 diatoms, and 4 brown algae. Screening their complete proteomes using hidden Markov models (HMMs) trained for MP detection resulted in over 4,000 MPs, with most species having between 65 and 100 putative MPs. Classification in clans and families according to the MEROPS database showed a highly diverse MP repertoire in each species. Analyses of domain composition, orthologous groups, distribution, and abundance within the stramenopile lineage revealed a few oomycete-specific MPs and MPs potentially related to lifestyle. In-depth analyses of MPs in the plant pathogen Phytophthora infestans revealed 91 MPs, divided over 21 protein families, including 25 MPs with a predicted signal peptide or signal anchor. Expression profiling showed different patterns of MP gene expression during pre-infection and infection stages. When expressed in leaves of Nicotiana benthamiana, 12 MPs changed the sizes of lesions caused by inoculation with P. infestans; with 9 MPs the lesions were larger, suggesting a positive effect on the virulence of P. infestans, while 3 MPs had a negative effect, resulting in smaller lesions. To the best of our knowledge, this is the first systematic inventory of MPs in oomycetes and the first study pinpointing MPs as potential pathogenicity factors in Phytophthora.
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Affiliation(s)
- Charikleia Schoina
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Present address:
Enza Zaden Research and Development B. V.EnkhuizenNetherlands
| | - Sander Y. A. Rodenburg
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Bioinformatics GroupWageningen University and ResearchWageningenNetherlands
- Present address:
The Hyve B. V.UtrechtNetherlands
| | - Harold J. G. Meijer
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Wageningen Plant ResearchWageningen University and ResearchWageningenNetherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Present address:
Theoretical Biology & Bioinformatics groupDepartment of BiologyUtrecht UniversityUtrechtNetherlands
| | - Lysette T. Lacambra
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Present address:
East‐West Seed Knowledge TransferNonthaburiThailand
| | - Klaas Bouwmeester
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Biosystematics GroupWageningen University and ResearchWageningenNetherlands
| | - Francine Govers
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
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8
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Mooney BC, Mantz M, Graciet E, Huesgen PF. Cutting the line: manipulation of plant immunity by bacterial type III effector proteases. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3395-3409. [PMID: 33640987 DOI: 10.1093/jxb/erab095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Pathogens and their hosts are engaged in an evolutionary arms race. Pathogen-derived effectors promote virulence by targeting components of a host's innate immune system, while hosts have evolved proteins that sense effectors and trigger a pathogen-specific immune response. Many bacterial effectors are translocated into host cells using type III secretion systems. Type III effector proteases irreversibly modify host proteins by cleavage of peptide bonds and are prevalent among both plant and animal bacterial pathogens. In plants, the study of model effector proteases has yielded important insights into the virulence mechanisms employed by pathogens to overcome their host's immune response, as well as into the mechanisms deployed by their hosts to detect these effector proteases and counteract their effects. In recent years, the study of a larger number of effector proteases, across a wider range of pathogens, has yielded novel insights into their functions and recognition. One key limitation that remains is the lack of methods to detect protease cleavage at the proteome-wide level. We review known substrates and mechanisms of plant pathogen type III effector proteases and compare their functions with those of known type III effector proteases of mammalian pathogens. Finally, we discuss approaches to uncover their function on a system-wide level.
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Affiliation(s)
- Brian C Mooney
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
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Frey AM, Chaput D, Shaw LN. Insight into the human pathodegradome of the V8 protease from Staphylococcus aureus. Cell Rep 2021; 35:108930. [PMID: 33826899 PMCID: PMC8054439 DOI: 10.1016/j.celrep.2021.108930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus possesses ten extracellular proteases with mostly unknown targets in the human proteome. To assist with bacterial protease target discovery, we have applied and compared two N-terminomics methods to investigate cleavage of human serum proteins by S. aureus V8 protease, discovering 85 host-protein targets. Among these are virulence-relevant complement, iron sequestration, clotting cascade, and host protease inhibitor proteins. Protein cleavage sites have been identified, providing insight into the disruption of host protein function by V8. Complement proteins are cleaved within peptidase and sushi domains, and host protease inhibitors are cleaved outside their protease-trapping motifs. Our data highlight the potential for further application of N-terminomics in discovery of bacterial protease substrates in other host niches and provide omics-scale insight into the role of the V8 protease in S. aureus pathogenesis. S. aureus-secreted proteases are central to disease causation, but the discovery of their host substrates has been limited. Frey et al. use N-terminomic approaches to uncover human serum targets of the V8 protease that are from virulence-relevant processes such as the host inflammatory network and nutrient sequestration.
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Affiliation(s)
- Andrew Michael Frey
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Dale Chaput
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey Neil Shaw
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
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10
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Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae. Sci Rep 2021; 11:6743. [PMID: 33762641 PMCID: PMC7990945 DOI: 10.1038/s41598-021-86217-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/23/2021] [Indexed: 01/31/2023] Open
Abstract
Mycoplasma pneumoniae is a significant cause of pneumonia and post infection sequelae affecting organ sites distant to the respiratory tract are common. It is also a model organism where extensive 'omics' studies have been conducted to gain insight into how minimal genome self-replicating organisms function. An N-terminome study undertaken here identified 4898 unique N-terminal peptides that mapped to 391 (56%) predicted M. pneumoniae proteins. True N-terminal sequences beginning with the initiating methionine (iMet) residue from the predicted Open Reading Frame (ORF) were identified for 163 proteins. Notably, almost half (317; 46%) of the ORFS derived from M. pneumoniae strain M129 are post-translationally modified, presumably by proteolytic processing, because dimethyl labelled neo-N-termini were characterised that mapped beyond the predicted N-terminus. An analysis of the N-terminome describes endoproteolytic processing events predominately targeting tryptic-like sites, though cleavages at negatively charged residues in P1' (D and E) with lysine or serine/alanine in P2' and P3' positions also occurred frequently. Surfaceome studies identified 160 proteins (23% of the proteome) to be exposed on the extracellular surface of M. pneumoniae. The two orthogonal methodologies used to characterise the surfaceome each identified the same 116 proteins, a 72% (116/160) overlap. Apart from lipoproteins, transporters, and adhesins, 93/160 (58%) of the surface proteins lack signal peptides and have well characterised, canonical functions in the cell. Of the 160 surface proteins identified, 134 were also targets of endo-proteolytic processing. These processing events are likely to have profound implications for how the host immune system recognises and responds to M. pneumoniae.
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11
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Wang Y, Jiang N, Wang B, Tao H, Zhang X, Guan Q, Liu C. Integrated Transcriptomic and Proteomic Analyses Reveal the Role of NprR in Bacillus anthracis Extracellular Protease Expression Regulation and Oxidative Stress Responses. Front Microbiol 2020; 11:590851. [PMID: 33362738 PMCID: PMC7756075 DOI: 10.3389/fmicb.2020.590851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
NprR is a protein of Bacillus anthracis that exhibits moonlighting functions as either a phosphatase or a neutral protease regulator that belongs to the RNPP family. We previously observed that the extracellular protease activity of an nprR deletion mutant significantly decreased within in vitro cultures. To identify the genes within the regulatory network of nprR that contribute to its protease activity, integrated transcriptomic and proteomic analyses were conducted here by comparing the nprR deletion mutant and parent strains. A total of 366 differentially expressed genes (DEGs) between the strains were observed via RNA-seq analysis. In addition, label-free LC-MS/MS analysis revealed 503 differentially expressed proteins (DEPs) within the intracellular protein fraction and 213 extracellular DEPs with significant expressional differences between the strains. The majority of DEGs and DEPs were involved in environmental information processing and metabolism. Integrated transcriptomic and proteomic analyses indicated that oxidation-reduction-related GO terms for intracellular DEPs and endopeptidase-related GO terms for extracellular DEPs were significantly enriched in the mutant strain. Notably, many genes involved in protease activity were largely downregulated in the nprR deletion mutant cultures. Moreover, western blot analysis revealed that the major extracellular neutral protease Npr599 was barely expressed in the nprR deletion mutant strain. The mutant also exhibited impaired degradation of protective antigen, which is a major B. anthracis toxin component, thereby resulting in higher protein yields. Concomitantly, another global transcriptional regulator, SpxA1, was also dramatically downregulated in the nprR deletion mutant, resulting in higher sensitivity to oxidative and disulfide stress. These data consequently indicate that NprR is a transcriptional regulator that controls genes whose products function as extracellular proteases and also is involved in oxidative stress responses. This study thus contributes to a more comprehensive understanding of the biological function of NprR, and especially in the middle growth stages of B. anthracis.
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Affiliation(s)
- Yanchun Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Na Jiang
- Beijing Fisheries Research Institute, Beijing, China
| | - Bowen Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Haoxia Tao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Qing Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Chunjie Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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12
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Citrullination-Resistant LL-37 Is a Potent Antimicrobial Agent in the Inflammatory Environment High in Arginine Deiminase Activity. Int J Mol Sci 2020; 21:ijms21239126. [PMID: 33266231 PMCID: PMC7730452 DOI: 10.3390/ijms21239126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
LL-37, the only member of the mammalian cathelicidin in humans, plays an essential role in innate immunity by killing pathogens and regulating the inflammatory response. However, at an inflammatory focus, arginine residues in LL-37 can be converted to citrulline via a reaction catalyzed by peptidyl-arginine deiminases (PAD2 and PAD4), which are expressed in neutrophils and are highly active during the formation of neutrophil extracellular traps (NETs). Citrullination impairs the bactericidal activity of LL-37 and abrogates its immunomodulatory functions. Therefore, we hypothesized that citrullination-resistant LL-37 variants would retain the functionality of the native peptide in the presence of PADs. To test this hypothesis, we synthetized LL-37 in which arginine residues were substituted by homoarginine (hArg-LL-37). Bactericidal activity of hArg-LL-37 was comparable with that of native LL-37, but neither treatment with PAD4 nor exposure to NETs affected the antibacterial and immunomodulatory activities of hArg-LL-37. Importantly, the susceptibilities of LL-37 and hArg-LL-37 to degradation by proteases did not significantly differ. Collectively, we demonstrated that citrullination-resistant hArg-LL-37 is an attractive lead compound for the generation of new agents to treat bacterial infections and other inflammatory diseases associated with enhanced PAD activity. Moreover, our results provide a proof-of-concept for synthesis of therapeutic peptides using homoarginine.
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Li G, Obeng E, Shu J, Shu J, Chen J, Wu Y, He Y. Genomic Variability and Post-translational Protein Processing Enhance the Immune Evasion of Mycoplasma hyopneumoniae and Its Interaction With the Porcine Immune System. Front Immunol 2020; 11:510943. [PMID: 33117335 PMCID: PMC7575705 DOI: 10.3389/fimmu.2020.510943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae, Mhp) is a geographically widespread and economically devastating pathogen that colonizes ciliated epithelium; the infection of Mhp can damnify the mucociliary functions as well as leading to Mycoplasma pneumonia of swine (MPS). MPS is a chronic respiratory infectious disease with high infectivity, and the mortality can be increased by secondary infections as the host immunity gets down-regulated during Mhp infection. The host immune responses are regarded as the main driving force for the disease development, while MPS is prone to attack repeatedly in farms even with vaccination or other treatments. As one of the smallest microorganisms with limited genome scale and metabolic pathways, Mhp can use several mechanisms to achieve immune evasion effect and derive enough nutrients from its host, indicating that there is a strong interaction between Mhp and porcine organism. In this review, we summarized the immune evasion mechanisms from genomic variability and post-translational protein processing. Besides, Mhp can induce the immune cells apoptosis by reactive oxygen species production, excessive nitric oxide (NO) release and caspase activation, and stimulate the release of cytokines to regulate inflammation. This article seeks to provide some new points to reveal the complicated interaction between the pathogen and host immune system with Mhp as a typical example, further providing some new strategies for the vaccine development against Mhp infection.
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Affiliation(s)
- Gaojian Li
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Enoch Obeng
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jinqi Shu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jianhong Shu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Hom-Sun Biosciences Co., Ltd., Shaoxing, China
| | - Jian Chen
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuehong Wu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yulong He
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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14
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Awad MM, Hutton ML, Quek AJ, Klare WP, Mileto SJ, Mackin K, Ly D, Oorschot V, Bosnjak M, Jenkin G, Conroy PJ, West N, Fulcher A, Costin A, Day CJ, Jennings MP, Medcalf RL, Sanderson-Smith M, Cordwell SJ, Law RHP, Whisstock JC, Lyras D. Human Plasminogen Exacerbates Clostridioides difficile Enteric Disease and Alters the Spore Surface. Gastroenterology 2020; 159:1431-1443.e6. [PMID: 32574621 DOI: 10.1053/j.gastro.2020.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS The protease plasmin is an important wound healing factor, but it is not clear how it affects gastrointestinal infection-mediated damage, such as that resulting from Clostridioides difficile. We investigated the role of plasmin in C difficile-associated disease. This bacterium produces a spore form that is required for infection, so we also investigated the effects of plasmin on spores. METHODS C57BL/6J mice expressing the precursor to plasmin, the zymogen human plasminogen (hPLG), or infused with hPLG were infected with C difficile, and disease progression was monitored. Gut tissues were collected, and cytokine production and tissue damage were analyzed by using proteomic and cytokine arrays. Antibodies that inhibit either hPLG activation or plasmin activity were developed and structurally characterized, and their effects were tested in mice. Spores were isolated from infected patients or mice and visualized using super-resolution microscopy; the functional consequences of hPLG binding to spores were determined. RESULTS hPLG localized to the toxin-damaged gut, resulting in immune dysregulation with an increased abundance of cytokines (such as interleukin [IL] 1A, IL1B, IL3, IL10, IL12B, MCP1, MP1A, MP1B, GCSF, GMCSF, KC, TIMP-1), tissue degradation, and reduced survival. Administration of antibodies that inhibit plasminogen activation reduced disease severity in mice. C difficile spores bound specifically to hPLG and active plasmin degraded their surface, facilitating rapid germination. CONCLUSIONS We found that hPLG is recruited to the damaged gut, exacerbating C difficile disease in mice. hPLG binds to C difficile spores, and, upon activation to plasmin, remodels the spore surface, facilitating rapid spore germination. Inhibitors of plasminogen activation might be developed for treatment of C difficile or other infection-mediated gastrointestinal diseases.
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Affiliation(s)
- Milena M Awad
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Melanie L Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Adam J Quek
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia
| | - William P Klare
- School of Life and Environmental Sciences and Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Steven J Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Kate Mackin
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Diane Ly
- Illawarra health and Medical Research Institute, Wollongong, Australia; School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, Australia
| | - Viola Oorschot
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia; Monash Micro Imaging, Monash University, Clayton, Australia
| | - Marijana Bosnjak
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Grant Jenkin
- Monash Infectious Diseases, Monash Health, Clayton, Australia
| | - Paul J Conroy
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia
| | - Nick West
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, St. Lucia, Australia
| | - Alex Fulcher
- Monash Micro Imaging, Monash University, Clayton, Australia
| | - Adam Costin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia
| | | | | | - Robert L Medcalf
- Molecular Neurotrauma and Haemostasis, Australian Centre for Blood Diseases, Monash University, Clayton, Australia
| | - Martina Sanderson-Smith
- Illawarra health and Medical Research Institute, Wollongong, Australia; School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences and Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Ruby H P Law
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia
| | - James C Whisstock
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging and Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Clayton, Australia; European Molecular Biology Laboratory Australia, Monash University, Clayton, Australia; South East University-Monash Joint Institute, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
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15
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Mercer DK, O'Neil DA. Innate Inspiration: Antifungal Peptides and Other Immunotherapeutics From the Host Immune Response. Front Immunol 2020; 11:2177. [PMID: 33072081 PMCID: PMC7533533 DOI: 10.3389/fimmu.2020.02177] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
The purpose of this review is to describe antifungal therapeutic candidates in preclinical and clinical development derived from, or directly influenced by, the immune system, with a specific focus on antimicrobial peptides (AMP). Although the focus of this review is AMP with direct antimicrobial effects on fungi, we will also discuss compounds with direct antifungal activity, including monoclonal antibodies (mAb), as well as immunomodulatory molecules that can enhance the immune response to fungal infection, including immunomodulatory AMP, vaccines, checkpoint inhibitors, interferon and colony stimulating factors as well as immune cell therapies. The focus of this manuscript will be a non-exhaustive review of antifungal compounds in preclinical and clinical development that are based on the principles of immunology and the authors acknowledge the incredible amount of in vitro and in vivo work that has been conducted to develop such therapeutic candidates.
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16
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Shumeiko V, Paltiel Y, Bisker G, Hayouka Z, Shoseyov O. A Paper-Based Near-Infrared Optical Biosensor for Quantitative Detection of Protease Activity Using Peptide-Encapsulated SWCNTs. SENSORS 2020; 20:s20185247. [PMID: 32937986 PMCID: PMC7570893 DOI: 10.3390/s20185247] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
A protease is an enzyme that catalyzes proteolysis of proteins into smaller polypeptides or single amino acids. As crucial elements in many biological processes, proteases have been shown to be informative biomarkers for several pathological conditions in humans, animals, and plants. Therefore, fast, reliable, and cost-effective protease biosensors suitable for point-of-care (POC) sensing may aid in diagnostics, treatment, and drug discovery for various diseases. This work presents an affordable and simple paper-based dipstick biosensor that utilizes peptide-encapsulated single-wall carbon nanotubes (SWCNTs) for protease detection. Upon enzymatic digestion of the peptide, a significant drop in the photoluminescence (PL) of the SWCNTs was detected. As the emitted PL is in the near-infrared region, the developed biosensor has a good signal to noise ratio in biological fluids. One of the diseases associated with abnormal protease activity is pancreatitis. In acute pancreatitis, trypsin concentration could reach up to 84 µg/mL in the urine. For proof of concept, we demonstrate the feasibility of the proposed biosensor for the detection of the abnormal levels of trypsin activity in urine samples.
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Affiliation(s)
- Vlad Shumeiko
- Department of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
| | - Yossi Paltiel
- Center for Nanoscience and Nanotechnology, Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel;
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel;
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
- Correspondence: (Z.H.); (O.S.)
| | - Oded Shoseyov
- Department of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
- Correspondence: (Z.H.); (O.S.)
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17
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Mulkern D, Hewitt A, Parker H, Batt J, Yonel Z, Grant MM. Predicted salivary human protease activity in experimental gingivitis revealed by endoProteo-FASP approach. Eur J Oral Sci 2020; 128:386-394. [PMID: 32794587 DOI: 10.1111/eos.12729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
Gingivitis is a highly prevalent oral condition that can be studied in humans via the 21-d experimental gingivitis model, which allows for investigations into the induction and resolution of gingivitis. In this study, we used the autolysis of saliva as a source of peptides to predict the activity of human proteases in saliva during induction and resolution of inflammation. Healthy volunteers, with no remarkable oral or systemic conditions, were recruited into the study and stimulated saliva samples were collected at days 0, 21, and 35 of experimental gingivitis. Plaque and gingival indices were recorded to ensure clinical induction and resolution. Saliva was auto-digested at 37°C for 18 h before identification of peptides by mass spectrometry. Protease prediction was carried out using Proteasix in silico with the identified peptides. A comparison of day 0 to days 21 and 35 showed changes in predicted protease activity. Correlation network analysis revealed that at day 21 the proteases became less connected and showed a potential for a dysregulated system; by day 35 the connectivity was returning towards similar conditions at day 0. This study demonstrates that changes in predicted proteases are apparent even in saliva collected from donors experiencing inflammation around three teeth.
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Affiliation(s)
- Dimitri Mulkern
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Amy Hewitt
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Hadyn Parker
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Joanna Batt
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Zehra Yonel
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Melissa M Grant
- Periodontal Research Group, School of Dentistry, University of Birmingham, Birmingham, UK
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18
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Master Sculptor at Work: Enteropathogenic Escherichia coli Infection Uniquely Modifies Mitochondrial Proteolysis during Its Control of Human Cell Death. mSystems 2020; 5:5/3/e00283-20. [PMID: 32487743 PMCID: PMC8534729 DOI: 10.1128/msystems.00283-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) causes severe diarrheal disease and is present globally. EPEC virulence requires a bacterial type III secretion system to inject >20 effector proteins into human intestinal cells. Three effectors travel to mitochondria and modulate apoptosis; however, the mechanisms by which effectors control apoptosis from within mitochondria are unknown. To identify and quantify global changes in mitochondrial proteolysis during infection, we applied the mitochondrial terminal proteomics technique mitochondrial stable isotope labeling by amino acids in cell culture-terminal amine isotopic labeling of substrates (MS-TAILS). MS-TAILS identified 1,695 amino N-terminal peptides from 1,060 unique proteins and 390 N-terminal peptides from 215 mitochondrial proteins at a false discovery rate of 0.01. Infection modified 230 cellular and 40 mitochondrial proteins, generating 27 cleaved mitochondrial neo-N termini, demonstrating altered proteolytic processing within mitochondria. To distinguish proteolytic events specific to EPEC from those of canonical apoptosis, we compared mitochondrial changes during infection with those reported from chemically induced apoptosis. During infection, fewer than half of all mitochondrial cleavages were previously described for canonical apoptosis, and we identified nine mitochondrial proteolytic sites not previously reported, including several in proteins with an annotated role in apoptosis, although none occurred at canonical Asp-Glu-Val-Asp (DEVD) sites associated with caspase cleavage. The identification and quantification of novel neo-N termini evidences the involvement of noncaspase human or EPEC protease(s) resulting from mitochondrial-targeting effectors that modulate cell death upon infection. All proteomics data are available via ProteomeXchange with identifier PXD016994. IMPORTANCE To our knowledge, this is the first study of the mitochondrial proteome or N-terminome during bacterial infection. Identified cleavage sites that had not been previously reported in the mitochondrial N-terminome and that were not generated in canonical apoptosis revealed a pathogen-specific strategy to control human cell apoptosis. These data inform new mechanisms of virulence factors targeting mitochondria and apoptosis during infection and highlight how enteropathogenic Escherichia coli (EPEC) manipulates human cell death pathways during infection, including candidate substrates of an EPEC protease within mitochondria. This understanding informs the development of new antivirulence strategies against the many human pathogens that target mitochondria during infection. Therefore, mitochondrial stable isotope labeling by amino acids in cell culture-terminal amine isotopic labeling of substrates (MS-TAILS) is useful for studying other pathogens targeting human cell compartments.
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19
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Isaiah S, Loots DT, Solomons R, van der Kuip M, Tutu Van Furth AM, Mason S. Overview of Brain-to-Gut Axis Exposed to Chronic CNS Bacterial Infection(s) and a Predictive Urinary Metabolic Profile of a Brain Infected by Mycobacterium tuberculosis. Front Neurosci 2020; 14:296. [PMID: 32372900 PMCID: PMC7186443 DOI: 10.3389/fnins.2020.00296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
A new paradigm in neuroscience has recently emerged - the brain-gut axis (BGA). The contemporary focus in this paradigm has been gut → brain ("bottom-up"), in which the gut-microbiome, and its perturbations, affects one's psychological state-of-mind and behavior, and is pivotal in neurodegenerative disorders. The emerging brain → gut ("top-down") concept, the subject of this review, proposes that dysfunctional brain health can alter the gut-microbiome. Feedback of this alternative bidirectional highway subsequently aggravates the neurological pathology. This paradigm shift, however, focuses upon non-communicable neurological diseases (progressive neuroinflammation). What of infectious diseases, in which pathogenic bacteria penetrate the blood-brain barrier and interact with the brain, and what is this effect on the BGA in bacterial infection(s) that cause chronic neuroinflammation? Persistent immune activity in the CNS due to chronic neuroinflammation can lead to irreversible neurodegeneration and neuronal death. The properties of cerebrospinal fluid (CSF), such as immunological markers, are used to diagnose brain disorders. But what of metabolic markers for such purposes? If a BGA exists, then chronic CNS bacterial infection(s) should theoretically be reflected in the urine. The premise here is that chronic CNS bacterial infection(s) will affect the gut-microbiome and that perturbed metabolism in both the CNS and gut will release metabolites into the blood that are filtered (kidneys) and excreted in the urine. Here we assess the literature on the effects of chronic neuroinflammatory diseases on the gut-microbiome caused by bacterial infection(s) of the CNS, in the context of information attained via metabolomics-based studies of urine. Furthermore, we take a severe chronic neuroinflammatory infectious disease - tuberculous meningitis (TBM), caused by Mycobacterium tuberculosis, and examine three previously validated CSF immunological biomarkers - vascular endothelial growth factor, interferon-gamma and myeloperoxidase - in terms of the expected changes in normal brain metabolism. We then model the downstream metabolic effects expected, predicting pivotal altered metabolic pathways that would be reflected in the urinary profiles of TBM subjects. Our cascading metabolic model should be adjustable to account for other types of CNS bacterial infection(s) associated with chronic neuroinflammation, typically prevalent, and difficult to distinguish from TBM, in the resource-constrained settings of poor communities.
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Affiliation(s)
- Simon Isaiah
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Du Toit Loots
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Regan Solomons
- Department of Pediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Martijn van der Kuip
- Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Academic Medical Center, Emma Children’s Hospital, Amsterdam, Netherlands
| | - A. Marceline Tutu Van Furth
- Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Academic Medical Center, Emma Children’s Hospital, Amsterdam, Netherlands
| | - Shayne Mason
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
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20
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Rosa N, Campos B, Esteves AC, Duarte AS, Correia MJ, Silva RM, Barros M. Tracking the functional meaning of the human oral-microbiome protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:199-235. [PMID: 32312422 DOI: 10.1016/bs.apcsb.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.
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Affiliation(s)
- Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Bruno Campos
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Cristina Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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21
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Haney EF, Barbosa SC, Baquir B, Hancock REW. Influence of Non-natural Cationic Amino Acids on the Biological Activity Profile of Innate Defense Regulator Peptides. J Med Chem 2019; 62:10294-10304. [DOI: 10.1021/acs.jmedchem.9b01344] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Evan F. Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Simone C. Barbosa
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Beverlie Baquir
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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22
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Chen D, Geis-Asteggiante L, Gomes FP, Ostrand-Rosenberg S, Fenselau C. Top-Down Proteomic Characterization of Truncated Proteoforms. J Proteome Res 2019; 18:4013-4019. [PMID: 31545043 DOI: 10.1021/acs.jproteome.9b00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A top-down proteomic strategy with semiautomated analysis of data sets has proven successful for the global identification of truncated proteins without the use of chemical derivatization, enzymatic manipulation, immunoprecipitation, or other enrichment. This approach provides the reliable identification of internal polypeptides formed from precursor gene products by proteolytic cleavage of both the N- and C-termini, as well as truncated proteoforms that retain one or the other termini. The strategy has been evaluated by application to the immunosuppressive extracellular vesicles released by myeloid-derived suppressor cells. More than 1000 truncated proteoforms have been identified, from which binding motifs are derived to allow characterization of the putative proteases responsible for truncation.
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Affiliation(s)
- Dapeng Chen
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Fabio P Gomes
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , Maryland 21250 , United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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23
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Ehrhardt K, Steck N, Kappelhoff R, Stein S, Rieder F, Gordon IO, Boyle EC, Braubach P, Overall CM, Finlay BB, Grassl GA. Persistent Salmonella enterica Serovar Typhimurium Infection Induces Protease Expression During Intestinal Fibrosis. Inflamm Bowel Dis 2019; 25:1629-1643. [PMID: 31066456 PMCID: PMC6749888 DOI: 10.1093/ibd/izz070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Intestinal fibrosis is a common and serious complication of Crohn's disease characterized by the accumulation of fibroblasts, deposition of extracellular matrix, and formation of scar tissue. Although many factors including cytokines and proteases contribute to the development of intestinal fibrosis, the initiating mechanisms and the complex interplay between these factors remain unclear. METHODS Chronic infection of mice with Salmonella enterica serovar Typhimurium was used to induce intestinal fibrosis. A murine protease-specific CLIP-CHIP microarray analysis was employed to assess regulation of proteases and protease inhibitors. To confirm up- or downregulation during fibrosis, we performed quantitative real-time polymerase chain reaction (PCR) and immunohistochemical stainings in mouse tissue and tissue from patients with inflammatory bowel disease. In vitro infections were used to demonstrate a direct effect of bacterial infection in the regulation of proteases. RESULTS Mice develop severe and persistent intestinal fibrosis upon chronic infection with Salmonella enterica serovar Typhimurium, mimicking the pathology of human disease. Microarray analyses revealed 56 up- and 40 downregulated proteases and protease inhibitors in fibrotic cecal tissue. Various matrix metalloproteases, serine proteases, cysteine proteases, and protease inhibitors were regulated in the fibrotic tissue, 22 of which were confirmed by quantitative real-time PCR. Proteases demonstrated site-specific staining patterns in intestinal fibrotic tissue from mice and in tissue from human inflammatory bowel disease patients. Finally, we show in vitro that Salmonella infection directly induces protease expression in macrophages and epithelial cells but not in fibroblasts. CONCLUSIONS In summary, we show that chronic Salmonella infection regulates proteases and protease inhibitors during tissue fibrosis in vivo and in vitro, and therefore this model is well suited to investigating the role of proteases in intestinal fibrosis.
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Affiliation(s)
- Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology and German Center for Infection Research (DZIF), Partner Site Hannover, Hannover Medical School, Hannover, Germany
| | - Natalie Steck
- Institute for Experimental Medicine, Christian-Albrechts University of Kiel, Kiel, Germany, and Research Center Borstel, Borstel, Germany
| | - Reinhild Kappelhoff
- Department of Oral Biological and Medical Sciences, Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Stephanie Stein
- Institute for Experimental Medicine, Christian-Albrechts University of Kiel, Kiel, Germany, and Research Center Borstel, Borstel, Germany,Present affiliation: Center for Internal Medicine, I. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Rieder
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute
| | - Ilyssa O Gordon
- Department of Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Erin C Boyle
- Department of Cardiothoracic, Transplantation, and Vascular Surgery, Hannover Medical School, Hannover, Germany,Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Peter Braubach
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Guntram A Grassl
- Institute of Medical Microbiology and Hospital Epidemiology and German Center for Infection Research (DZIF), Partner Site Hannover, Hannover Medical School, Hannover, Germany,Address correspondence to: Guntram A. Grassl, PhD, Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany ()
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24
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Hurtado Silva M, Berry IJ, Strange N, Djordjevic SP, Padula MP. Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets. Proteomes 2019; 7:proteomes7020011. [PMID: 30934878 PMCID: PMC6631386 DOI: 10.3390/proteomes7020011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.
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Affiliation(s)
- Mariella Hurtado Silva
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Iain J Berry
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Natalie Strange
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Steven P Djordjevic
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Matthew P Padula
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
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25
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Tangsongcharoen C, Roytrakul S, Smith DR. Analysis of cellular proteome changes in response to ZIKV NS2B-NS3 protease expression. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:89-97. [PMID: 30391636 DOI: 10.1016/j.bbapap.2018.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/05/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
Abstract
The recent emergence of Zika virus (ZIKV) has caused global concern as a result of the association with neurological disorders, and brain development dysfunction in fetuses of mothers who become infected with ZIKV during pregnancy. The NS2B-NS3 protease is important for viral replication and offers an attractive drug target. In addition to processing the viral polypeptide, evidence has shown that the NS2B-NS3 protease also targets cellular proteins as part of the viral replication process. This study sought to determine new host cell protein targets of ZIKV NS2B-NS3 (zNS2B-NS3). Plasmids encoding the protease domains of zNS2B-NS3pro and an inactive zNS2B-NS3(S135A) were transfected into HEK293T/17 cells and differentially expressed proteins were detected by 2D gel electrophoresis. A total of 18 protein spots were observed as differentially expressed between zNS2B-NS3pro and zNS2B-NS3(S135A), of which 7 were selected for identification by mass spectrometry. Four proteins (protein disulfide-isomerase A3 (PDIA3), heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1), voltage-dependent anion-selective channel (VDAC) and aldolase A (ALDOA)) were selected for validation by independent transient expression and western blot analysis. Three proteins (PDIA3, hnRNP A2/B1 and ALDOA) were successfully validated, but only two proteins (PDIA3 and ALDOA) were shown to be regulated in ZIKV infection in agreement with the results of the transfection experiments. This study has identified two proteins, PDIA3 an ALDOA whose expression is modulated by the ZIKV NS2B-NS3 protease, and these proteins are involved in the ER stress response and glycolysis respectively, two critical cellular processes in ZIKV infection.
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Affiliation(s)
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.
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26
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Klychnikov OI, Shamorkina TM, Weeks SD, van Leeuwen HC, Corver J, Drijfhout JW, van Veelen PA, Sluchanko NN, Strelkov SV, Hensbergen PJ. Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family. J Biol Chem 2018; 293:11154-11165. [PMID: 29794027 DOI: 10.1074/jbc.ra118.003244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/22/2018] [Indexed: 12/20/2022] Open
Abstract
Pro-Pro endopeptidases (PPEPs) belong to a recently discovered family of proteases capable of hydrolyzing a Pro-Pro bond. The first member from the bacterial pathogen Clostridium difficile (PPEP-1) cleaves two C. difficile cell-surface proteins involved in adhesion, one of which is encoded by the gene adjacent to the ppep-1 gene. However, related PPEPs may exist in other bacteria and may shed light on substrate specificity in this enzyme family. Here, we report on the homolog of PPEP-1 in Paenibacillus alvei, which we denoted PPEP-2. We found that PPEP-2 is a secreted metalloprotease, which likewise cleaved a cell-surface protein encoded by an adjacent gene. However, the cleavage motif of PPEP-2, PLP↓PVP, is distinct from that of PPEP-1 (VNP↓PVP). As a result, an optimal substrate peptide for PPEP-2 was not cleaved by PPEP-1 and vice versa. To gain insight into the specificity mechanism of PPEP-2, we determined its crystal structure at 1.75 Å resolution and further confirmed the structure in solution using small-angle X-ray scattering (SAXS). We show that a four-amino-acid loop, which is distinct in PPEP-1 and -2 (GGST in PPEP-1 and SERV in PPEP-2), plays a crucial role in substrate specificity. A PPEP-2 variant, in which the four loop residues had been swapped for those from PPEP-1, displayed a shift in substrate specificity toward PPEP-1 substrates. Our results provide detailed insights into the PPEP-2 structure and the structural determinants of substrate specificity in this new family of PPEP proteases.
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Affiliation(s)
- Oleg I Klychnikov
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | | | - Stephen D Weeks
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | | | | | - Jan W Drijfhout
- Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, The Netherlands
| | | | - Nikolai N Sluchanko
- the A. N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia, and.,the Department of Biophysics, Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergei V Strelkov
- From the Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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27
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Jalomo-Khayrova E, Mares RE, Muñoz PLA, Meléndez-López SG, Rivero IA, Ramos MA. Soluble expression of an amebic cysteine protease in the cytoplasm of Escherichia coli SHuffle Express cells and purification of active enzyme. BMC Biotechnol 2018; 18:20. [PMID: 29615011 PMCID: PMC5883314 DOI: 10.1186/s12896-018-0429-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background Recombinant production of amebic cysteine proteases using Escherichia coli cells as the bacterial system has become a challenging effort, with protein insolubility being the most common issue. Since many of these enzymes need a native conformation stabilized by disulfide bonds, an elaborate process of oxidative folding is usually demanded to get a functional protein. The cytoplasm of E. coli SHuffle Express cells owns an enhanced ability to properly fold proteins with disulfide bonds. Because of this cellular feature, it was possible to assume that this strain represents a reliable expression system and worthwhile been considered as an efficient bacterial host for the recombinant production of amebic cysteine proteases. Results Using E. coli SHuffle Express cells as the bacterial system, we efficiently produce soluble recombinant EhCP1protein. Enzymatic and inhibition analyses revealed that it exhibits proper catalytic abilities, proceeds effectively over the substrate (following an apparent Michaelis-Menten kinetics), and displays a typical inhibition profile. Conclusions We report the first feasibility study of the recombinant production of amebic cysteine proteases using E. coli SHuffle Express as the bacterial host. We present a simple protocol for the recombinant expression and purification of fully soluble and active EhCP1 enzyme. We confirm the suitability of recombinant EhCP1 as a therapeutic target. We propose an approachable bacterial system for the recombinant production of amebic proteins, particularly for those with a need for proper oxidative folding. Electronic supplementary material The online version of this article (10.1186/s12896-018-0429-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Jalomo-Khayrova
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, México
| | - Rosa E Mares
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, México
| | - Patricia L A Muñoz
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, México
| | - Samuel G Meléndez-López
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, México
| | - Ignacio A Rivero
- Centro de Graduados e Investigación en Química, Instituto Tecnológico de Tijuana, Boulevard Industrial S/N, Mesa de Otay, 22510, Tijuana, BCN, México
| | - Marco A Ramos
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, México.
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28
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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29
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Tholey A, Taylor NL, Heazlewood JL, Bendixen E. We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project. J Proteome Res 2017; 16:4273-4280. [DOI: 10.1021/acs.jproteome.7b00408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Nicolas L. Taylor
- Australian
Research Council Centre of Excellence in Plant Energy Biology, School
of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Joshua L. Heazlewood
- School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Emøke Bendixen
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 Aarhus, Denmark
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30
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Berry IJ, Jarocki VM, Tacchi JL, Raymond BBA, Widjaja M, Padula MP, Djordjevic SP. N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen. Sci Rep 2017; 7:11063. [PMID: 28894154 PMCID: PMC5593965 DOI: 10.1038/s41598-017-11296-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022] Open
Abstract
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.
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Affiliation(s)
- Iain J Berry
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Veronica M Jarocki
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Jessica L Tacchi
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Benjamin B A Raymond
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Michael Widjaja
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia. .,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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31
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Tholey A, Becker A. Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2191-2199. [PMID: 28711385 DOI: 10.1016/j.bbamcr.2017.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 02/06/2023]
Abstract
Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Alexander Becker
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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32
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Cristea IM. The Host-Pathogen Ecosystem Viewed Through the Prism of Proteomics. Mol Cell Proteomics 2017; 16:S1-S4. [PMID: 28283547 DOI: 10.1074/mcp.e117.068270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/10/2017] [Indexed: 12/29/2022] Open
Affiliation(s)
- Ileana M Cristea
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
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