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Hu DD, Weaver SD, Collars OA, Champion PA, Champion MM. N-terminal proteomics of Mycobacterium marinum using bottom-up label-free quantitative analysis in data-dependent acquisition mode on a timsTOF Pro mass spectrometer. Microbiol Resour Announc 2024; 13:e0126323. [PMID: 38477461 PMCID: PMC11008207 DOI: 10.1128/mra.01263-23] [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: 12/21/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
N-terminal acetylation in Mycobacterium tuberculosis is correlated with pathogenic activity. We used genomics and bottom-up proteomics to identify protein Emp1 as the sole acetyltransferase responsible for acetylation of EsxA, a known virulence factor. Using custom data analysis, we screened the proteome to identify 22 additional putative substrates of Emp1.
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Affiliation(s)
- Daniel D. Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Simon D. Weaver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Owen A. Collars
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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2
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Collars OA, Jones BS, Hu DD, Weaver SD, Sherman TA, Champion MM, Champion PA. An N-acetyltransferase required for ESAT-6 N-terminal acetylation and virulence in Mycobacterium marinum. mBio 2023; 14:e0098723. [PMID: 37772840 PMCID: PMC10653941 DOI: 10.1128/mbio.00987-23] [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: 04/25/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE N-terminal acetylation is a protein modification that broadly impacts basic cellular function and disease in higher organisms. Although bacterial proteins are N-terminally acetylated, little is understood how N-terminal acetylation impacts bacterial physiology and pathogenesis. Mycobacterial pathogens cause acute and chronic disease in humans and in animals. Approximately 15% of mycobacterial proteins are N-terminally acetylated, but the responsible enzymes are largely unknown. We identified a conserved mycobacterial protein required for the N-terminal acetylation of 23 mycobacterial proteins including the EsxA virulence factor. Loss of this enzyme from M. marinum reduced macrophage killing and spread of M. marinum to new host cells. Defining the acetyltransferases responsible for the N-terminal protein acetylation of essential virulence factors could lead to new targets for therapeutics against mycobacteria.
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Affiliation(s)
- Owen A. Collars
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, Indiana, USA
| | - Bradley S. Jones
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, Indiana, USA
| | - Daniel D. Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Simon D. Weaver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Taylor A. Sherman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew M. Champion
- Eck Institute for Global Health, University of Note Dame, Notre Dame, Indiana, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, Indiana, USA
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3
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Pal M, Yadav VK, Pal P, Agarwal N, Rao A. The physiological effect of rimI/rimJ silencing by CRISPR interference in Mycobacterium smegmatis mc 2155. Arch Microbiol 2023; 205:211. [PMID: 37119317 DOI: 10.1007/s00203-023-03561-5] [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: 01/15/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
N-terminal acetylation of proteins is an important post-translational modification (PTM) found in eukaryotes and prokaryotes. In bacteria, N-terminal acetylation is suggested to play various regulatory roles related to protein stability, gene expression, stress response, and virulence; however, the mechanism of such response remains unclear. The proteins, namely RimI/RimJ, are involved in N-terminal acetylation in mycobacteria. In this study, we used CRISPR interference (CRISPRi) to silence rimI/rimJ in Mycobacterium smegmatis mc2155 to investigate the physiological effects of N-terminal acetylation in cell survival and stress response. Repeat analysis of growth curves in rich media and biofilm analysis in minimal media of various mutant strains and wild-type bacteria did not show significant differences that could be attributed to the rimI/rimJ silencing. However, total proteome and acetylome profiles varied significantly across mutants and wild-type strains, highlighting the role of RimI/RimJ in modulating levels of proprotein acetylation in the cellular milieu. Further, we observed a significant increase in the minimum inhibitory concentration (MIC) (from 64 to 1024 µg ml-1) for the drug isoniazid in rimI mutant strains. The increase in MIC value for the drug isoniazid in the mutant strains suggests the link between N-terminal acetylation and antibiotic resistance. The study highlights the utility of CRISPRi as a convenient tool to study the role of PTMs, such as acetylation in mycobacteria. It also identifies rimI/rimJ genes as necessary for managing cellular response against antibiotic stress. Further research would be required to decipher the potential of targeting acetylation to enhance the efficacy of existing antibiotics.
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Grants
- BT/PR25690/GET/119/142/2017 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR25690/GET/119/142/2017 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR25690/GET/119/142/2017 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR25690/GET/119/142/2017 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR25690/GET/119/142/2017 Department of Biotechnology, Ministry of Science and Technology, India
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Affiliation(s)
- Mohinder Pal
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
| | - Vinay Kumar Yadav
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pramila Pal
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, 496, UdyogVihar Phase-III, Gurgaon, Haryana, 122016, India
| | - Nisheeth Agarwal
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, 496, UdyogVihar Phase-III, Gurgaon, Haryana, 122016, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
- Academy of Scientific and Innovation Research (AcSIR), Kamla Nehru Nagar, Sector 19, Ghaziabad, 201002, Uttar Pradesh, India.
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4
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Collars OA, Jones BS, Hu DD, Weaver SD, Champion MM, Champion PA. An N-acetyltransferase required for EsxA N-terminal protein acetylation and virulence in Mycobacterium marinum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532585. [PMID: 36993388 PMCID: PMC10055061 DOI: 10.1101/2023.03.14.532585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
N-terminal protein acetylation is a ubiquitous post-translational modification that broadly impacts diverse cellular processes in higher organisms. Bacterial proteins are also N-terminally acetylated, but the mechanisms and consequences of this modification in bacteria are poorly understood. We previously quantified widespread N-terminal protein acetylation in pathogenic mycobacteria (C. R. Thompson, M. M. Champion, and P.A. Champion, J Proteome Res 17(9): 3246-3258, 2018, https:// doi: 10.1021/acs.jproteome.8b00373). The major virulence factor EsxA (ESAT-6, Early secreted antigen, 6kDa) was one of the first N-terminally acetylated proteins identified in bacteria. EsxA is conserved in mycobacterial pathogens, including Mycobacterium tuberculosis and Mycobacterium marinum, a non-tubercular mycobacterial species that causes tuberculosis-like disease in ectotherms. However, enzyme responsible for EsxA N-terminal acetylation has been elusive. Here, we used genetics, molecular biology, and mass-spectroscopy based proteomics to demonstrate that MMAR_1839 (renamed Emp1, ESX-1 modifying protein, 1) is the putative N-acetyl transferase (NAT) solely responsible for EsxA acetylation in Mycobacterium marinum. We demonstrated that ERD_3144, the orthologous gene in M. tuberculosis Erdman, is functionally equivalent to Emp1. We identified at least 22 additional proteins that require Emp1 for acetylation, demonstrating that this putative NAT is not dedicated to EsxA. Finally, we showed that loss of emp1 resulted in a significant reduction in the ability of M. marinum to cause macrophage cytolysis. Collectively, this study identified a NAT required for N-terminal acetylation in Mycobacterium and provided insight into the requirement of N-terminal acetylation of EsxA and other proteins in mycobacterial virulence in the macrophage.
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Affiliation(s)
- Owen A. Collars
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, USA
| | - Bradley S. Jones
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, USA
| | - Daniel D. Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, USA
| | - Simon D. Weaver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, USA
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
- Eck Institute for Global Health, University of Note Dame, Notre Dame, USA
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5
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Mousseau CB, Pierre CA, Hu DD, Champion MM. Miniprep assisted proteomics (MAP) for rapid proteomics sample preparation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:916-924. [PMID: 36373982 PMCID: PMC9933840 DOI: 10.1039/d2ay01549h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/28/2022] [Indexed: 06/14/2023]
Abstract
Complete enzymatic digestion of proteins for bottom-up proteomics is substantially improved by use of detergents for denaturation and solubilization. Detergents however, are incompatible with many proteases and highly detrimental to LC-MS/MS. Recently; filter-based methods have seen wide use due to their capacity to remove detergents and harmful reagents prior to digestion and mass spectrometric analysis. We hypothesized that non-specific protein binding to negatively charged silica-based filters would be enhanced by addition of lyotropic salts, similar to DNA purification. We sought to exploit these interactions and investigate if low-cost DNA purification spin-filters, 'Minipreps,' efficiently and reproducibly bind proteins for digestion and LC-MS/MS analysis. We propose a new method, Miniprep Assisted Proteomics (MAP), for sample preparation. We demonstrate binding capacity, performance, recovery and identification rates for proteins and whole-cell lysates using MAP. MAP recovered equivalent or greater protein yields from 0.5-50 μg analyses benchmarked against commercial trapping preparations. Nano UHPLC-MS/MS proteome profiling of lysates of Escherichia coli had 99.3% overlap vs. existing approaches and reproducibility of replicate minipreps was 98.8% at the 1% FDR protein level. Label Free Quantitative proteomics was performed and 91.2% of quantified proteins had a %CV <20% (2044/2241). Miniprep Assisted Proteomics can be performed in minutes, shows low variability, high recovery and proteome depth. This suggests a significant role for adventitious binding in developing new proteomics sample preparation techniques. MAP represents an efficient, ultra-low-cost alternative for sample preparation in a commercially obtainable device that costs ∼$0.50 (USD) per miniprep.
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Affiliation(s)
- C Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Camille A Pierre
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA.
- Berthiaume Institute for Precision Health, University of Notre Dame, Notre Dame, IN 46556, USA
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6
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Wang R, Wang Z, Lu H. Separation methods for system-wide profiling of protein terminome. Proteomics 2023; 23:e2100374. [PMID: 35997653 DOI: 10.1002/pmic.202100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Protein N- and C-termini have specific biochemical properties and functions. They play vital roles in various biological processes, such as protein stability and localization. In addition, post-translational modifications and proteolytic processing generate different proteoforms at protein termini. In recent years, terminomics has attracted significant attention, and numerous strategies have been developed to achieve high-throughput and global terminomics analysis. This review summarizes the recent protein N-termini and C-termini enrichment methods and their application in different samples. We also look ahead further application of terminomics in profiling protease substrates and discovery of disease biomarkers and therapeutic targets.
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Affiliation(s)
- Rui Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, People's Republic of China
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7
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Fernández E, Bogaert A, Timmerman E, Staes A, Impens F, Gevaert K. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms. Methods Mol Biol 2022; 2477:293-309. [PMID: 35524124 DOI: 10.1007/978-1-0716-2257-5_17] [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: 06/14/2023]
Abstract
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.
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Affiliation(s)
- Esperanza Fernández
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Bogaert
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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8
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Parks AR, Escalante-Semerena JC. Protein N-terminal acylation: An emerging field in bacterial cell physiology. CURRENT TRENDS IN MICROBIOLOGY 2022; 16:1-18. [PMID: 37009250 PMCID: PMC10062008 DOI: 10.31300/ctmb.16.2022.1-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
N-terminal (Nt)-acylation is the irreversible addition of an acyl moiety to the terminal alpha amino group of a peptide chain. This type of modification alters the nature of the N terminus, which can interfere with the function of the modified protein by disrupting protein interactions, function, localization, degradation, hydrophobicity, or charge. Nt acylation is found in all domains of life and is a highly common occurrence in eukaryotic cells. However, in prokaryotes very few cases of Nt acylation have been reported. It was once thought that Nt acylation of proteins, other than ribosomal proteins, was uncommon in prokaryotes, but recent evidence suggests that this modification may be more common than once realized. In this review, we discuss what is known about prokaryotic Nt acetylation and the acetyltransferases that are responsible, as well as recent advancements in this field and currently used methods to study Nt acetylation.
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Affiliation(s)
- Anastacia R. Parks
- Department of Microbiology, University of Georgia, Athens, GA 30606, USA
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9
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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10
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Smith SM, Gilbert JL. Interfacial compliance, energy dissipation, frequency effects, and long-term fretting corrosion performance of Ti-6Al-4V/CoCrMo interfaces. J Biomed Mater Res A 2021; 110:409-423. [PMID: 34402604 DOI: 10.1002/jbm.a.37299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/14/2021] [Accepted: 08/05/2021] [Indexed: 11/10/2022]
Abstract
Fretting corrosion in modular orthopedic implants is a well-documented process that may be associated with adverse local tissue reactions, pain, and revisions. Engineering modular junction interfaces to withstand applied fretting motion without surface abrasion could prevent implant degradation and surface damage. Previous work on geometrically modified Ti-6Al-4V/CoCrMo interfaces with increased compliance showed reduced fretting currents and surface damage during short term, variable-load in vitro testing. This study assesses the same interfaces under long-term conditions using an in vitro pin-on-disk fretting corrosion test apparatus. Preliminary variable-load frequency testing of typical control pin geometries showed a frequency-dependent current response, with underlying contact conditions of metal-metal interfaces that remained unchanged. One-million-cycle testing showed diminished fretting currents in all groups by 5 × 105 cycles, but consistently lower currents in the high-compliance group. Corresponding fretting currents and work of fretting measurements of high-compliance pins confirmed that minimal fretting was experienced at the interface, with elastic bending of the pin accounting for almost all applied displacement. Debris generated during testing were composed of titanium and chromium oxides, small amounts of cobalt and molybdenum oxides, and sodium and phosphate originating from the surrounding test solution. Post-test analyses of sample surfaces revealed substantially more surface damage on CoCrMo disks than Ti-6Al-4V pins, thought to be a result of adhesive wear of mixed oxide debris on the pin and abrasion of the disk by the oxide debris layer. Surface damage to high-compliance pins suggests some abrasion is unavoidable with geometric modifications.
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Affiliation(s)
- Stephanie M Smith
- Clemson-MUSC Bioengineering Program, Department of Bioengineering, Clemson University and the Medical University of South Carolina, Charleston, South Carolina, USA
| | - Jeremy L Gilbert
- Clemson-MUSC Bioengineering Program, Department of Bioengineering, Clemson University and the Medical University of South Carolina, Charleston, South Carolina, USA
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11
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Labella M, Castells M. Hypersensitivity reactions and anaphylaxis to checkpoint inhibitor-monoclonal antibodies and desensitization. Ann Allergy Asthma Immunol 2021; 126:623-629. [PMID: 33781937 DOI: 10.1016/j.anai.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVE To review type 1 hypersensitivity reactions and anaphylaxis to checkpoint inhibitor-monoclonal antibodies and its management with drug desensitization. DATA SOURCES English-language literature on MEDLINE regarding hypersensitivity, anaphylaxis, and checkpoint inhibitor-monoclonal antibodies. STUDY SELECTIONS References were selected based on relevance, novelty, robustness, and applicability. RESULTS There are well-known tissue toxicities associated to checkpoint inhibitors, but hypersensitivity reactions and anaphylaxis have been underreported. The presentation of these reactions is based on clinical phenotypes with underlying endotypes identified by specific biomarkers. Drug desensitizations have been successfully applied to checkpoint inhibitor drugs to allow patients with cancer to receive first-line therapies. This review provides current best practices for the recognition and diagnosis of hypersensitivity reactions and anaphylaxis to checkpoint inhibitors and their management using drug desensitization. CONCLUSION Hypersensitivity reactions and anaphylaxis have been identified as potential adverse effects induced by checkpoint inhibitor-monoclonal antibodies. Drug desensitization is a safe and effective treatment option for patients who experience hypersensitivity reactions in need of these monoclonal antibodies to improve cancer outcomes.
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Affiliation(s)
- Marina Labella
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain; Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain.
| | - Mariana Castells
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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12
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Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
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13
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Role of nano-sensitizers in radiation therapy of metastatic tumors. Cancer Treat Res Commun 2021; 26:100303. [PMID: 33454575 DOI: 10.1016/j.ctarc.2021.100303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Cancer metastasis remains the major cause of global cancer deaths. Radiation therapy remains one of the golden standards for cancer treatment. Nanomedicine based strategies have been designed and developed in order to improve the clinical outcomes of cancer therapy and diagnosis at molecular levels. Over the years, several researchers have shown their interest in using radiosensitizers made of high Z elements. Metal-based nanosystems also play a dual role by enhancing the synergistic effect of cell killing via various biological immune responses. This review summarizes the role of Nano-sensitizers in boosting radiation (ionizing/non-ionizing radiations) induced biological responses in treatment of metastatic cancer models.
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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Abstract
Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery.
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Modulation of the bacterial CobB sirtuin deacylase activity by N-terminal acetylation. Proc Natl Acad Sci U S A 2020; 117:15895-15901. [PMID: 32571932 DOI: 10.1073/pnas.2005296117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eukaryotic cells, the N-terminal amino moiety of many proteins is modified by N-acetyltransferases (NATs). This protein modification can alter the folding of the target protein; can affect binding interactions of the target protein with substrates, allosteric effectors, or other proteins; or can trigger protein degradation. In prokaryotes, only ribosomal proteins are known to be N-terminally acetylated, and the acetyltransferases responsible for this modification belong to the Rim family of proteins. Here, we report that, in Salmonella enterica, the sirtuin deacylase CobB long isoform (CobBL) is N-terminally acetylated by the YiaC protein of this bacterium. Results of in vitro acetylation assays showed that CobBL was acetylated by YiaC; liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to confirm these results. Results of in vitro and in vivo experiments showed that CobBL deacetylase activity was negatively affected when YiaC acetylated its N terminus. We report 1) modulation of a bacterial sirtuin deacylase activity by acetylation, 2) that the Gcn5-related YiaC protein is the acetyltransferase that modifies CobBL, and 3) that YiaC is an NAT. Based on our data, we propose the name of NatA (N-acyltransferase A) in lieu of YiaC to reflect the function of the enzyme.
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A New ESX-1 Substrate in Mycobacterium marinum That Is Required for Hemolysis but Not Host Cell Lysis. J Bacteriol 2019; 201:JB.00760-18. [PMID: 30833360 DOI: 10.1128/jb.00760-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The ESX-1 (ESAT-6 system 1) secretion system plays a conserved role in the virulence of diverse mycobacterial pathogens, including the human pathogen Mycobacterium tuberculosis and M. marinum, an environmental mycobacterial species. The ESX-1 system promotes the secretion of protein virulence factors to the extracytoplasmic environment. The secretion of these proteins triggers the host response by lysing the phagosome during macrophage infection. Using proteomic analyses of the M. marinum secretome in the presence and absence of a functional ESX-1 system, we and others have hypothesized that MMAR_2894, a PE family protein, is a potential ESX-1 substrate in M. marinum We used genetic and quantitative proteomic approaches to determine if MMAR_2894 is secreted by the ESX-1 system, and we defined the requirement of MMAR_2894 for ESX-1-mediated secretion and virulence. We show that MMAR_2894 is secreted by the ESX-1 system in M. marinum and is itself required for the optimal secretion of the known ESX-1 substrates in M. marinum Moreover, we found that MMAR_2894 was differentially required for hemolysis and cytolysis of macrophages, two lytic activities ascribed to the M. marinum ESX-1 system.IMPORTANCE Both Mycobacterium tuberculosis, the cause of human tuberculosis (TB), and Mycobacterium marinum, a pathogen of ectotherms, use the ESX-1 secretion system to cause disease. There are many established similarities between the ESX-1 systems in M. tuberculosis and in M. marinum Yet the two bacteria infect different hosts, hinting at species-specific functions of the ESX-1 system. Our findings demonstrate that MMAR_2894 is a PE protein secreted by the ESX-1 system of M. marinum We show that MMAR_2894 is required for the optimal secretion of mycobacterial proteins required for disease. Because the MMAR_2894 gene is not conserved in M. tuberculosis, our findings demonstrate that MMAR_2894 may contribute to a species-specific function of the ESX-1 system in M. marinum, providing new insight into how the M. marinum and M. tuberculosis systems differ.
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Misal SA, Li S, Tang H, Radivojac P, Reilly JP. Identification of N-terminal protein processing sites by chemical labeling mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1015-1023. [PMID: 30884002 PMCID: PMC6522274 DOI: 10.1002/rcm.8435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/01/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Proteins undergo post-translational modifications and proteolytic processing that can affect their biological function. Processing often involves the loss of single residues. Cleavage of signal peptides from the N-terminus is commonly associated with translocation. Recent reports have suggested that other processing sites also exist. METHODS The secreted proteins from S. aureus N315 were precipitated with trichloroacetic acid (TCA) and amidinated with S-methyl thioacetimidate (SMTA). Amidinated proteins were digested with trypsin and analyzed with a high-resolution orbitrap mass spectrometer. RESULTS Sixteen examples of Staphylococcus aureus secretory proteins that lose an N-terminal signal peptide during their export were identified using this amidination approach. The N-termini of proteins with and without methionine were identified. Unanticipated protein cleavages due to sortase and an unknown protease were also uncovered. CONCLUSIONS A simple N-terminal amidination based mass spectrometry approach is described that facilitates identification of the N-terminus of a mature protein and the discovery of unexpected processing sites.
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Affiliation(s)
- Santosh A Misal
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Sujun Li
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Haixu Tang
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Predrag Radivojac
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
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