1
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Alexander N, McDonald L, Wesdemiotis C, Pang Y. Native mass spectrometry analysis of conjugated HSA and BSA complexes with various flavonoids. Analyst 2024; 149:1929-1938. [PMID: 38376111 PMCID: PMC10926777 DOI: 10.1039/d3an02070c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 02/21/2024]
Abstract
Mass spectrometry was used to study the binding interaction between serum albumin proteins (BSA and HSA) and flavone dyes, which is known to induce large fluorescence signals for protein detection. By electrospray ionization mass spectrometry (ESI-MS), multiple charged species/states could be produced in ammonium acetate buffer, while preserving the native structures of the proteins. Subsequent introduction of a flavone dye into the buffered solution resulted in an immediate interaction, forming the respective protein-dye conjugates associated by non-covalent interactions. Formation of protein-dye conjugates induced a notable response in the ESI-MS spectra, including changes in both the charge states and molecular mass of the protein species. The resulting data pointed out that the protein-flavone dye maintained a 1 : 1 ratio in the conjugate, although multiple binding sites for drug molecules are present in albumin proteins.
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Affiliation(s)
| | - Lucas McDonald
- Department of Chemistry, The University of Akron, OH 44325, USA.
| | | | - Yi Pang
- Department of Chemistry, The University of Akron, OH 44325, USA.
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2
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Jiang FF, Wang RQ, Guo CY, Zheng K, Long-Liu H, Su L, Xie SS, Chen HC, Liu ZF. Phospho-proteomics identifies a critical role of ATF2 in pseudorabies virus replication. Virol Sin 2022; 37:591-600. [PMID: 35688418 PMCID: PMC9437614 DOI: 10.1016/j.virs.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 06/02/2022] [Indexed: 11/02/2022] Open
Abstract
Pseudorabies virus (PRV), an etiological agent of pseudorabies in livestock, has negatively affected the porcine industry all over the world. Epithelial cells are reported as the first site of PRV infection. However, the role of host proteins and its related signaling pathways in PRV replication is largely unclear. In this study, we performed a quantitative phosphoproteomics screening on PRV-infected porcine kidney (PK-15) epithelial cells. Totally 5723 phosphopeptides, corresponding to 2180 proteins, were obtained, and the phosphorylated states of 810 proteins were significantly different in PRV-infected cells compared with mock-infected cells (P < 0.05). GO and KEGG analysis revealed that these differentially expressed phosphorylated proteins were predominantly related to RNA transport and MAPK signaling pathways. Further functional studies of NF-κB, transcription activator factor-2 (ATF2), MAX and SOS genes in MAPK signaling pathway were analyzed using RNA interference (RNAi) knockdown. It showed that only ATF2-knockdown reduces both PRV titer and viral genome copy number. JNK pathway inhibition and CRISPR/Cas9 gene knockout showed that ATF2 was required for the effective replication of PRV, especially during the biogenesis of viral genome DNA. Subsequently, by overexpression of the ATF2 gene and point mutation of the amino acid positions 69/71 of ATF2, it was further demonstrated that the phosphorylation of ATF2 promoted PRV replication. These findings suggest that ATF2 may provide potential therapeutic target for inhibiting PRV infection. Phosphoproteomic profiling of PRV-infected PK-15 cells with iTRAQ-quantification. JNK pathway regulates ATF2 phosphorylation and PRV replication. Phosphorylation of ATF2 promotes PRV replication.
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3
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Rex DAB, Chanderasekaran J, Rai AB, Phukan H, Sarma A, Prasad TSK, Madanan MG. Leptospira and Leptospirosis: New Systems Science Insights on Proteome, Posttranslational Modifications, and Pathogen-Host Interaction. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:280-289. [PMID: 35446144 DOI: 10.1089/omi.2022.0007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Leptospirosis is one of the most important zoonotic diseases for planetary health. It is caused by Leptospira spp., which poses a formidable challenge in both rural and urban geographies. Discovery of molecular targets is crucial for developing interventions, including vaccines, against leptospirosis. We report here novel systems science insights on Leptospira proteome, posttranslational modifications (PTMs), and pathogen-host interactions, with an eye to bacterial pathophysiology from a functional standpoint. A systematic reanalysis of unassigned spectra from our previous total proteome identification was used for a multi-PTM search. Notably, we identified 3693 unique high-confidence PTM sites corresponding to 1266 proteins (PTM-profiling probability cutoff value ≥75%). The majority of the phosphorylated peptides were found to be GroEL molecular chaperones. Notably, the molecular docking of PTM-GroEL with STAT3, an important signaling protein in cytokine production, resulted in the prediction of druggable "hotspots." These energetically significant smaller subsets of amino acids (hotspot residues) offer promise for practical applications in planetary health, rational drug design, and peptide engineering. Furthermore, the prediction strategies described here could serve as a starting point for narrowing down the more extensive interface in protein-protein interactions that currently exist. Going forward, systems science approaches and the new insights reported here offer veritable prospects for innovation in preventing and treating leptospirosis.
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Affiliation(s)
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Jaikanth Chanderasekaran
- Department of Pharmacology, School of Pharmacy and Technology Management, SVKM'S NMIMS University, Hyderabad, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Homen Phukan
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
| | - Abhijit Sarma
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
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4
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Westermann AJ, Vogel J. Cross-species RNA-seq for deciphering host-microbe interactions. Nat Rev Genet 2021; 22:361-378. [PMID: 33597744 DOI: 10.1038/s41576-021-00326-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
The human body is constantly exposed to microorganisms, which entails manifold interactions between human cells and diverse commensal or pathogenic bacteria. The cellular states of the interacting cells are decisive for the outcome of these encounters such as whether bacterial virulence programmes and host defence or tolerance mechanisms are induced. This Review summarizes how next-generation RNA sequencing (RNA-seq) has become a primary technology to study host-microbe interactions with high resolution, improving our understanding of the physiological consequences and the mechanisms at play. We illustrate how the discriminatory power and sensitivity of RNA-seq helps to dissect increasingly complex cellular interactions in time and space down to the single-cell level. We also outline how future transcriptomics may answer currently open questions in host-microbe interactions and inform treatment schemes for microbial disorders.
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Affiliation(s)
- Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
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5
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Rauh T, Brameyer S, Kielkowski P, Jung K, Sieber SA. MS-Based in Situ Proteomics Reveals AMPylation of Host Proteins during Bacterial Infection. ACS Infect Dis 2020; 6:3277-3289. [PMID: 33259205 PMCID: PMC9558369 DOI: 10.1021/acsinfecdis.0c00740] [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] [Indexed: 01/26/2023]
Abstract
![]()
Bacteria utilize versatile strategies
to propagate infections within
human cells, e.g., by the injection of effector proteins,
which alter crucial signaling pathways. One class of such virulence-associated
proteins is involved in the AMPylation of eukaryotic Rho GTPases with
devastating effects on viability. In order to get an inventory of
AMPylated proteins, several technologies have been developed. However,
as they were designed for the analysis of cell lysates, knowledge
about AMPylation targets in living cells is largely lacking. Here,
we implement a chemical-proteomic method for deciphering AMPylated
host proteins in situ during bacterial infection.
HeLa cells treated with a previously established cell permeable pronucleotide
probe (pro-N6pA) were infected with Vibrio parahaemolyticus, and modified host proteins were identified upon probe enrichment
and LC-MS/MS analysis. Three already known targets of the AMPylator
VopS—Rac1, RhoA, and Cdc42—could be confirmed, and several
other Rho GTPases were additionally identified. These hits were validated
in comparative studies with V. parahaemolyticus wild type and a mutant producing an inactive VopS (H348A). The method
further allowed to decipher the sites of modification and facilitated
a time-dependent analysis of AMPylation during infection. Overall,
the methodology provides a reliable detection of host AMPylation in situ and thus a versatile tool in monitoring infection
processes.
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Affiliation(s)
- Theresa Rauh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Sophie Brameyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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6
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Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:97-125. [PMID: 32951817 PMCID: PMC7320668 DOI: 10.1016/bs.apcsb.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.
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7
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Tatli M, Hebert AS, Coon JJ, Amador-Noguez D. Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N 2-Fixing Conditions. Front Microbiol 2019; 10:1986. [PMID: 31551951 PMCID: PMC6737584 DOI: 10.3389/fmicb.2019.01986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022] Open
Abstract
Protein phosphorylation is a post-translational modification with widespread regulatory roles in both eukaryotes and prokaryotes. Using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins, belonging to major pathways such as glycolysis, TCA cycle, electron transport, nitrogen metabolism, and protein synthesis. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across growth conditions. For example, we observed increased phosphorylation of nearly all glycolytic enzymes and a large fraction of ribosomal proteins during aerobic and N2-fixing conditions. We also observed substantial changes in the phosphorylation status of enzymes and regulatory proteins involved in nitrogen fixation and ammonia assimilation during N2-fixing conditions, including nitrogenase, the Rnf electron transport complex, the transcription factor NifA, GS-GOGAT cycle enzymes, and the PII regulatory protein. This suggested that protein phosphorylation may play an important role at regulating all aspects of nitrogen metabolism in Z. mobilis. This study provides new knowledge regarding the specific pathways and cellular processes that may be regulated by protein phosphorylation in this important industrial organism and provides a useful road map for future experiments that investigate the physiological role of specific phosphorylation events in Z. mobilis.
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Affiliation(s)
- Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Alexander S Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Genome Center of Wisconsin, Madison, WI, United States
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.,Morgridge Institute for Research, Madison, WI, United States
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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8
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Marcelino I, Colomé-Calls N, Holzmuller P, Lisacek F, Reynaud Y, Canals F, Vachiéry N. Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis. Front Microbiol 2019; 10:450. [PMID: 30930869 PMCID: PMC6429767 DOI: 10.3389/fmicb.2019.00450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 01/31/2023] Open
Abstract
Unraveling which proteins and post-translational modifications (PTMs) affect bacterial pathogenesis and physiology in diverse environments is a tough challenge. Herein, we used mass spectrometry-based assays to study protein phosphorylation and glycosylation in Ehrlichia ruminantium Gardel virulent (ERGvir) and attenuated (ERGatt) variants and, how they can modulate Ehrlichia biological processes. The characterization of the S/T/Y phosphoproteome revealed that both strains share the same set of phosphoproteins (n = 58), 36% being overexpressed in ERGvir. The percentage of tyrosine phosphorylation is high (23%) and 66% of the identified peptides are multi-phosphorylated. Glycoproteomics revealed a high percentage of glycoproteins (67% in ERGvir) with a subset of glycoproteins being specific to ERGvir (n = 64/371) and ERGatt (n = 36/343). These glycoproteins are involved in key biological processes such as protein, amino-acid and purine biosynthesis, translation, virulence, DNA repair, and replication. Label-free quantitative analysis revealed over-expression in 31 proteins in ERGvir and 8 in ERGatt. While further PNGase digestion confidently localized 2 and 5 N-glycoproteins in ERGvir and ERGatt, respectively, western blotting suggests that many glycoproteins are O-GlcNAcylated. Twenty-three proteins were detected in both the phospho- and glycoproteome, for the two variants. This work represents the first comprehensive assessment of PTMs on Ehrlichia biology, rising interesting questions regarding ER–host interactions. Phosphoproteome characterization demonstrates an increased versatility of ER phosphoproteins to participate in different mechanisms. The high number of glycoproteins and the lack of glycosyltransferases-coding genes highlight ER dependence on the host and/or vector cellular machinery for its own protein glycosylation. Moreover, these glycoproteins could be crucial to interact and respond to changes in ER environment. PTMs crosstalk between of O-GlcNAcylation and phosphorylation could be used as a major cellular signaling mechanism in ER. As little is known about the Ehrlichia proteins/proteome and its signaling biology, the results presented herein provide a useful resource for further hypothesis-driven exploration of Ehrlichia protein regulation by phosphorylation and glycosylation events. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD012589.
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Affiliation(s)
- Isabel Marcelino
- CIRAD, UMR ASTRE, Petit-Bourg, France.,ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,Unitè TReD-Path (Transmission Rèservoirs et Diversitè des Pathogènes), Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Núria Colomé-Calls
- Proteomics Laboratory, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Philippe Holzmuller
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,CIRAD, UMR ASTRE, Montpellier, France
| | - Frédérique Lisacek
- Proteome Informatics, Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department and Section of Biology, University of Geneva, Geneva, Switzerland
| | - Yann Reynaud
- Unitè TReD-Path (Transmission Rèservoirs et Diversitè des Pathogènes), Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Francesc Canals
- Proteomics Laboratory, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Nathalie Vachiéry
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,CIRAD, UMR ASTRE, Montpellier, France
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9
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Microbial Proteomics and Their Importance in Medical Microbiology. RECENT DEVELOPMENTS IN APPLIED MICROBIOLOGY AND BIOCHEMISTRY 2019. [PMCID: PMC7149639 DOI: 10.1016/b978-0-12-816328-3.00003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial infection is a leading cause of death around the world. Most of the infectious diseases are caused by drug-resistant microbes; this may lead to a delay in the administration of microbiologically effective therapy (Chen et al., 2017; Del Chierico et al., 2014). Therefore, exhaustive understanding of microbial physiologies, infection and defense systems, and survival strategies is of great interest in order to actively defeat microbial infection. Microbial proteomics provides complete information of microbial physiology and expression and function of the proteins that are involved in infection and also gives a clue in clinical diagnosis and antimicrobial therapy (Pérez-Llarena and Bou, 2016; Vranakis et al., 2014). Microbial proteomics helps to identify the proteins associated with microbial activity, microbial host-pathogen interactions, and antimicrobial resistant mechanism. Microbial activity of pathogens can be confirmed by using the 2-D gel-based and gel-free method with the combination of MALDI-TOF-LC-MS/MS. Proteomic analysis of microbial host-pathogen interaction reveals valuable information about the virulence of the pathogen and its resistance; it helps in better understanding of the infection and for developing strategies against microbial infections (Cheng et al., 2016). Fig. 3.1 schematically illustrates the proteomic analysis of the bacterial samples.
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10
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A decade of Nucleic Acid Programmable Protein Arrays (NAPPA) availability: News, actors, progress, prospects and access. J Proteomics 2018; 198:27-35. [PMID: 30553075 DOI: 10.1016/j.jprot.2018.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022]
Abstract
Understanding the dynamic of the proteome is a critical challenge because it requires high sensitive methodologies in high-throughput formats in order to decipher its modifications and complexity. While molecular biology provides relevant information about cell physiology that may be reflected in post-translational changes, High-Throughput (HT) experimental proteomic techniques are essential to provide valuable functional information of the proteins, peptides and the interconnections between them. Hence, many methodological developments and innovations have been reported during the last decade. To study more dynamic protein networks and fine interactions, Nucleic Acid Programmable Protein Arrays (NAPPA) was introduced a decade ago. The tool is rapidly maturing and serving as a gateway to characterize biological systems and diseases thanks primarily to its accuracy, reproducibility, throughput and flexibility. Currently, NAPPA technology has proved successful in several research areas adding valuable information towards innovative diagnostic and therapeutic applications. Here, the basic and latest advances within this modern technology in basic, translational research are reviewed, in addition to presenting its exciting new directions. Our final goal is to encourage more scientists/researchers to incorporate this method, which can help to remove bottlenecks in their particular research or biomedical projects. SIGNIFICANCE: Nucleic Acid Programmable Protein Arrays (NAPPA) is becoming an essential tool for functional proteomics and protein-protein interaction studies. The technology impacts decisively on projects aiming massive screenings and the latest innovations like the multiplexing capability or printing consistency make this a promising method to be integrated in novel and combinatorial proteomic approaches.
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11
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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12
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Ye X, Pan T, Wang D, Fang L, Ma J, Zhu X, Shi Y, Zhang K, Zheng H, Chen H, Li K, Xiao S. Foot-and-Mouth Disease Virus Counteracts on Internal Ribosome Entry Site Suppression by G3BP1 and Inhibits G3BP1-Mediated Stress Granule Assembly via Post-Translational Mechanisms. Front Immunol 2018; 9:1142. [PMID: 29887867 PMCID: PMC5980976 DOI: 10.3389/fimmu.2018.01142] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious, severe viral illness notifiable to the World Organization for Animal Health. The causative agent, FMD virus (FMDV), replicates rapidly and efficiently inhibits host translation and the innate immune response for it has developed multiple tactics to evade host defenses and takes over gene expression machinery in the host cell. Here, we report a systemic analysis of the proteome and phosphoproteome of FMDV-infected cells. Bioinformatics analysis suggested that FMDV infection shuts off host cap-dependent translation, but leaves intact internal ribosome entry site (IRES)-mediated translation for viral proteins. Interestingly, several FMDV IRES-transacting factors, including G3BP stress granule assembly factor 1 (G3BP1), were dephosphorylated during FMDV infection. Ectopic expression of G3BP1 inhibited FMDV IRES activity, promoted assembly of stress granules, and activated innate immune responses, collectively suppressing FMDV replication. To counteract these host protective responses, FMDV-induced dephosphorylation of G3BP1, compromising its inhibitory effect on viral IRES. In addition, FMDV also proteolytically cleaved G3BP1 by its 3C protease (3Cpro). G3BP1 was cleaved at glutamic acid-284 (E284) by FMDV 3Cpro, and this cleavage completely lost the abilities of G3BP1 to activate innate immunity and to inhibit FMDV replication. Together, these data provide new insights into the post-translational mechanisms by which FMDV limits host stress and antiviral responses and indicate that G3BP1 dephosphorylation and its proteolysis by viral protease are important factors in the failure of host defense against FMDV infection.
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Affiliation(s)
- Xu Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ting Pan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jun Ma
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xinyu Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yanling Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Keshan Zhang
- National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Kui Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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13
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Ni H, Fan W, Li C, Wu Q, Hou H, Hu D, Zheng F, Zhu X, Wang C, Cao X, Shao ZQ, Pan X. Streptococcus suis DivIVA Protein Is a Substrate of Ser/Thr Kinase STK and Involved in Cell Division Regulation. Front Cell Infect Microbiol 2018; 8:85. [PMID: 29616196 PMCID: PMC5869912 DOI: 10.3389/fcimb.2018.00085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/02/2018] [Indexed: 12/14/2022] Open
Abstract
Streptococcus suis serotype 2 is an important swine pathogen and an emerging zoonotic agent that causes severe infections. Recent studies have reported a eukaryotic-like Ser/Thr protein kinase (STK) gene and characterized its role in the growth and virulence of different S. suis 2 strains. In the present study, phosphoproteomic analysis was adopted to identify substrates of the STK protein. Seven proteins that were annotated to participate in different cell processes were identified as potential substrates, which suggests the pleiotropic effects of stk on S. suis 2 by targeting multiple pathways. Among them, a protein characterized as cell division initiation protein (DivIVA) was further investigated. In vitro analysis demonstrated that the recombinant STK protein directly phosphorylates threonine at amino acid position 199 (Thr-199) of DivIVA. This effect could be completely abolished by the T199A mutation. To determine the specific role of DivIVA in growth and division, a divIVA mutant was constructed. The ΔdivIVA strain exhibited impaired growth and division, including lower viability, enlarged cell mass, asymmetrical division caused by aberrant septum, and extremely weak pathogenicity in a mouse infection model. Collectively, our results reveal that STK regulates the cell growth and virulence of S. suis 2 by targeting substrates that are involved in different biological pathways. The inactivation of DivIVA leads to severe defects in cell division and strongly attenuates pathogenicity, thereby indicating its potential as a molecular drug target against S. suis.
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Affiliation(s)
- Hua Ni
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,School of Life Sciences, Nanjing Normal University, Nanjing, China.,The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges and Universities Under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar University, Kashgar, China
| | - Weiwei Fan
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,Department of Pharmacy, Changzhou Wujin People's Hospital, Changzhou, China
| | - Chaolong Li
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qianqian Wu
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Hongfen Hou
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Dan Hu
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Feng Zheng
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Xuhui Zhu
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Changjun Wang
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China
| | - Xiangrong Cao
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhu-Qing Shao
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiuzhen Pan
- Department of Microbiology, Hua Dong Research Institute for Medicine and Biotechnics, Nanjing, China.,School of Life Sciences, Nanjing Normal University, Nanjing, China
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14
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Manning AJ, Lee J, Wolfgeher DJ, Kron SJ, Greenberg JT. Simple strategies to enhance discovery of acetylation post-translational modifications by quadrupole-orbitrap LC-MS/MS. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:224-229. [DOI: 10.1016/j.bbapap.2017.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/07/2017] [Accepted: 10/13/2017] [Indexed: 12/26/2022]
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15
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Development of an activity-based probe for acyl-protein thioesterases. PLoS One 2018; 13:e0190255. [PMID: 29364904 PMCID: PMC5783350 DOI: 10.1371/journal.pone.0190255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/12/2017] [Indexed: 12/24/2022] Open
Abstract
Protein palmitoylation is a dynamic post-translational modification (PTM) important for cellular functions such as protein stability, trafficking, localization, and protein-protein interactions. S-palmitoylation occurs via the addition of palmitate to cysteine residues via a thioester linkage, catalyzed by palmitoyl acyl transferases (PATs), with removal of the palmitate catalyzed by acyl protein thioesterases (APTs) and palmitoyl-protein thioesterases (PPTs). Tools that target the regulators of palmitoylation–PATs, APTs and PPTs–will improve understanding of this essential PTM. Here, we describe the synthesis and application of a cell-permeable activity-based probe (ABP) that targets APTs in intact mammalian cells and the parasite Toxoplasma gondii. Using a focused library of substituted chloroisocoumarins, we identified a probe scaffold with nanomolar affinity for human APTs (HsAPT1 and HsAPT2) and synthesized a fluorescent ABP, JCP174-BODIPY TMR (JCP174-BT). We use JCP174-BT to profile HsAPT activity in situ in mammalian cells, to detect an APT in T. gondii (TgPPT1). We show discordance between HsAPT activity levels and total protein concentration in some cell lines, indicating that total protein levels may not be representative of APT activity in complex systems, highlighting the utility of this probe.
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16
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Farris TR, Zhu B, Wang JY, McBride JW. Ehrlichia chaffeensis TRP32 Nucleomodulin Function and Localization Is Regulated by NEDD4L-Mediated Ubiquitination. Front Cell Infect Microbiol 2018; 7:534. [PMID: 29376035 PMCID: PMC5768648 DOI: 10.3389/fcimb.2017.00534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 12/22/2017] [Indexed: 12/13/2022] Open
Abstract
Ehrlichia chaffeensis is an obligately intracellular bacterium that reprograms the mononuclear phagocyte through diverse effector-host interactions to modulate various host cell processes. In a previous study, we reported that the E. chaffeensis nucleomodulin TRP32 regulates transcription of host genes in several biologically relevant categories, including cell differentiation and proliferation. In this study, we investigate the effect of ubiquitination on TRP32 function and localization within the host cell. TRP32 is both mono- and polyubiquitinated on multiple lysine residues during infection and when ectopically expressed. Despite lacking a canonical PPxY motif, TRP32 interacted with, and was modified by the human HECT E3 ubiquitin (Ub) ligase NEDD4L. TRP32 ubiquitination was not by K48-linked polyUb chains, nor was it degraded by the proteasome; however, TRP32 was modified by K63-linked polyUb chains detected both in the cytosol and nucleus. HECT ligase inhibitor, heclin, altered the subnuclear localization of ectopically expressed TRP32 from a diffuse nuclear pattern to a lacy, punctate pattern with TRP32 distributed around the periphery of the nucleus and nucleoli. When a TRP32 lysine null (K-null) mutant was ectopically expressed, it exhibited a similar phenotype as single lysine mutants (K63R, K93R, and K123R). However, the K-null mutant showed increased amounts of cytoplasmic TRP32 compared to single lysine mutants or heclin-treated cells ectopically expressing TRP32. These alterations in localization corresponded to changes in TRP32 transcriptional repressor function with heclin-treated and single lysine mutants unable to repress transcription of a TRP32 target genes in a luciferase assay.
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Affiliation(s)
- Tierra R Farris
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Bing Zhu
- Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jennifer Y Wang
- Cell Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jere W McBride
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States.,Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Cell Biology, University of Texas Medical Branch, Galveston, TX, United States.,Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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17
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Exoproteomics of Pathogens: Analysis of Toxins and Other Virulence Factors by Proteomics. Methods Enzymol 2017; 586:211-227. [PMID: 28137564 DOI: 10.1016/bs.mie.2016.09.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Pathogens are known to release in their environment a large range of toxins and other virulence factors. Their pathogenicity relies on this arsenal of exoproteins and their orchestrated release upon changing environmental conditions. Exoproteomics aims at describing and quantifying the proteins found outside of the cells, thus takes advantage of the most recent methodologies of next-generation proteomics. This approach has been applied with great success to a variety of pathogens increasing the fundamental knowledge on pathogenicity. In this chapter, we describe how the exoproteome should be prepared and handled for high-throughput identification of exoproteins and their quantitation by label-free shotgun proteomics. We also mentioned some bioinformatics tools for extracting information such as toxin similarity search.
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18
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Kotewicz KM, Ramabhadran V, Sjoblom N, Vogel JP, Haenssler E, Zhang M, Behringer J, Scheck RA, Isberg RR. A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication. Cell Host Microbe 2016; 21:169-181. [PMID: 28041930 DOI: 10.1016/j.chom.2016.12.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 02/07/2023]
Abstract
Intracellular pathogens manipulate host organelles to support replication within cells. For Legionella pneumophila, the bacterium translocates proteins that establish an endoplasmic reticulum (ER)-associated replication compartment. We show here that the bacterial Sde proteins target host reticulon 4 (Rtn4) to control tubular ER dynamics, resulting in tubule rearrangements as well as alterations in Rtn4 associated with the replication compartment. These rearrangements are triggered via Sde-promoted ubiquitin transfer to Rtn4, occurring almost immediately after bacterial uptake. Ubiquitin transfer requires two sequential enzymatic activities from a single Sde polypeptide: an ADP-ribosyltransferase and a nucleotidase/phosphohydrolase. The ADP-ribosylated moiety of ubiquitin is a substrate for the nucleotidase/phosphohydrolase, resulting in either transfer of ubiquitin to Rtn4 or phosphoribosylation of ubiquitin in the absence of a ubiquitination target. Therefore, a single bacterial protein drives a multistep biochemical pathway to control ubiquitination and tubular ER function independently of the host ubiquitin machinery.
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Affiliation(s)
- Kristin M Kotewicz
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Vinay Ramabhadran
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA; Howard Hughes Medical Institute, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Nicole Sjoblom
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eva Haenssler
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Mengyun Zhang
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Jessica Behringer
- Program in Genetics, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Rebecca A Scheck
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA; Howard Hughes Medical Institute, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA.
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19
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Kasap M, Karadenizli A, Akpınar G, Uzuner H, Ayimugu A, Karaosmanoğlu K, Er DK. Comparative Analysis of Proteome Patterns of Francisella tularensis Isolates from Patients and the Environment. Curr Microbiol 2016; 74:230-238. [PMID: 27990601 DOI: 10.1007/s00284-016-1178-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/07/2016] [Indexed: 01/08/2023]
Abstract
Francisella tularensis is the causative agent of tularemia. Although major contributors and the main mechanism of the virulence are well known, some of the molecular details are still missing. Proteomics studies regarding F. tularensis have provided snapshot pictures of the organism grown under different culture conditions to understand the mechanism of virulence. In general, such studies were carried out with standard strains e.g., LVS and did not involve comparisons of F. tularensis isolates from either clinical or environmental sources. In this study, we performed two-dimensional gel electrophoresis (2DE)-based proteomic analysis and compared the protein profiles of the F. tularensis subsp. holarctica strains isolated from the clinical and the environmental samples. Regulations were detected in 14 spots when twofold regulation criteria were applied. The regulated protein spots were subjected to MALDI-TOF/TOF analysis and identified. Classification of the identified proteins based on metabolic functions revealed that the translation machinery was the most varying metabolic processes among the isolates. Using normalized protein spot intensities, PCA analysis was also performed. The results indicated that the strain isolated from water source was different then the strains isolated from the patients. Most interestingly, the isolates were strikingly distinguishable from the standard NCTC 10857 strain.
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Affiliation(s)
- Murat Kasap
- Medical Biology Department/DEKART Proteomics Laboratory, Kocaeli University Medical Faculty, Umuttepe, Kocaeli, 41380, Turkey
| | - Aynur Karadenizli
- Department of Medical Microbiology, Kocaeli University Medical Faculty, Umuttepe, Kocaeli, 41380, Turkey.
| | - Gürler Akpınar
- Medical Biology Department/DEKART Proteomics Laboratory, Kocaeli University Medical Faculty, Umuttepe, Kocaeli, 41380, Turkey
| | - Hüseyin Uzuner
- Department of Medical Microbiology, Kocaeli University Medical Faculty, Umuttepe, Kocaeli, 41380, Turkey
| | - Abula Ayimugu
- Department of Biomedical Engineering, Kocaeli University Technology Faculty, Kocaeli, Turkey
| | - Kübra Karaosmanoğlu
- Department of Biomedical Engineering, Kocaeli University Technology Faculty, Kocaeli, Turkey
| | - Doğanhan Kadir Er
- Department of Medical Microbiology, Kocaeli University Medical Faculty, Umuttepe, Kocaeli, 41380, Turkey
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20
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Morin-Sardin S, Jany JL, Artigaud S, Pichereau V, Bernay B, Coton E, Madec S. Proteomic analysis of the adaptative response of Mucor spp. to cheese environment. J Proteomics 2016; 154:30-39. [PMID: 27940316 DOI: 10.1016/j.jprot.2016.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/27/2016] [Accepted: 12/02/2016] [Indexed: 12/27/2022]
Abstract
In the cheese industry context, Mucor species exhibit an ambivalent behavior as some species are essential "technological" organisms of some cheeses while others can be spoiling agents. Previously, we observed that cheese "technological" species exhibited higher optimal growth rates on cheese related matrices than on synthetic media. This growth pattern combined with morphological differences raise the question of their adaptation to cheese. In this study, using a comparative proteomic approach, we described the metabolic pathways of three Mucor strains considered as "technological" or "contaminant" in the cheese environment (M. lanceolatus UBOCC-A-109153, M. racemosus UBOCC-A-109155, M. circinelloides CBS 277-49) as well as a non-cheese related strain (M. endophyticus CBS 385-95). Overall, 15.8 to 19.0% of the proteomes showed a fold change ≥1.6 in Potato Dextrose Agar (PDA) versus Cheese Agar (CA), a cheese mimicking-medium. The 289 differentially expressed proteins identified by LC MS-MS analysis were mostly assigned to energy and amino-acid metabolisms in PDA whereas a higher diversity of biological processes was observed for cheese related strains in CA. Surprisingly, the vast majority (72.9%) of the over-accumulated proteins were different according to the considered medium and strain. These results strongly suggest that the observed better adaptative response of "technological" strains to cheese environment is mediated by species-specific proteins. BIOLOGICAL SIGNIFICANCE The Mucor genus consists of a multitude of poorly known species. In the food context, few species are known for their positive role in the production of various food products, including cheese, while others are spoiling agents. The present study focused on the analysis of morphological and proteome differences of various Mucor spp. representative strains known as either positively (hereafter referred as "technological") or negatively (hereafter referred as "contaminant") associated with cheese or non-related to cheese (endophyte) on two different media, a synthetic medium and a cheese-mimicking medium. The main goal was to assess if adaptative traits of "technological" strains to the cheese environment could be identified. This work was based on observations we did in a recently published physiological study (Morin-Sardin et al., 2016). One of the important innovative aspects lies in the use for the first time of an extensive 2-DE approach to compare proteome variations for 4 strains on two different media. Results obtained offered an insight in the metabolic mechanisms associated with growth on a given medium and showed that adaptation to cheese environment is probably supported by species-specific proteins. The obtained data represent an essential step point for more targeted studies at the genomic and transcriptomic levels.
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Affiliation(s)
- Stéphanie Morin-Sardin
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Sébastien Artigaud
- Université de Brest, UMR 6539, Laboratoire des Sciences de l'Environnement Marin, LEMAR CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, 29280 Plouzané, France
| | - Vianney Pichereau
- Université de Brest, UMR 6539, Laboratoire des Sciences de l'Environnement Marin, LEMAR CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, 29280 Plouzané, France
| | - Benoît Bernay
- Plateforme Proteogen SFR ICORE, Université de Caen Basse-Normandie, 14032 Caen Cedex, France
| | - Emmanuel Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Stéphanie Madec
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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21
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Ye J, Zhang H, He W, Zhu B, Zhou D, Chen Z, Ashraf U, Wei Y, Liu Z, Fu ZF, Chen H, Cao S. Quantitative phosphoproteomic analysis identifies the critical role of JNK1 in neuroinflammation induced by Japanese encephalitis virus. Sci Signal 2016; 9:ra98. [DOI: 10.1126/scisignal.aaf5132] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Soares NC, Blackburn JM. Mass Spectrometry Targeted Assays as a Tool to Improve Our Understanding of Post-translational Modifications in Pathogenic Bacteria. Front Microbiol 2016; 7:1216. [PMID: 27540373 PMCID: PMC4972818 DOI: 10.3389/fmicb.2016.01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nelson C. Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa
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