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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: 43] [Impact Index Per Article: 14.3] [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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Khodadadi E, Zeinalzadeh E, Taghizadeh S, Mehramouz B, Kamounah FS, Khodadadi E, Ganbarov K, Yousefi B, Bastami M, Kafil HS. Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies. Infect Drug Resist 2020; 13:1785-1806. [PMID: 32606829 PMCID: PMC7305820 DOI: 10.2147/idr.s238446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Song K, Gras C, Capin G, Gimber N, Lehmann M, Mohd S, Puchkov D, Rödiger M, Wilhelmi I, Daumke O, Schmoranzer J, Schürmann A, Krauss M. A SEPT1-based scaffold is required for Golgi integrity and function. J Cell Sci 2019; 132:132/3/jcs225557. [PMID: 30709970 PMCID: PMC6382012 DOI: 10.1242/jcs.225557] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/17/2018] [Indexed: 12/13/2022] Open
Abstract
Compartmentalization of membrane transport and signaling processes is of pivotal importance to eukaryotic cell function. While plasma membrane compartmentalization and dynamics are well known to depend on the scaffolding function of septin GTPases, the roles of septins at intracellular membranes have remained largely elusive. Here, we show that the structural and functional integrity of the Golgi depends on its association with a septin 1 (SEPT1)-based scaffold, which promotes local microtubule nucleation and positioning of the Golgi. SEPT1 function depends on the Golgi matrix protein GM130 (also known as GOLGA2) and on centrosomal proteins, including CEP170 and components of γ-tubulin ring complex (γ-Turc), to facilitate the perinuclear concentration of Golgi membranes. Accordingly, SEPT1 depletion triggers a massive fragmentation of the Golgi ribbon, thereby compromising anterograde membrane traffic at the level of the Golgi.
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Affiliation(s)
- Kyungyeun Song
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Molecular Pharmacology and Cell Biology, 13125 Berlin, Germany
| | - Claudia Gras
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Molecular Pharmacology and Cell Biology, 13125 Berlin, Germany
| | - Gabrielle Capin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Molecular Pharmacology and Cell Biology, 13125 Berlin, Germany
| | - Niclas Gimber
- Charité Universitätsmedizin Berlin, Advanced Medical Bioimaging Core Facility - AMBIO, 10117 Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Cellular Imaging Facility, 13125 Berlin, Germany
| | - Saif Mohd
- Max-Delmbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Cellular Imaging Facility, 13125 Berlin, Germany
| | - Maria Rödiger
- Deutsches Institut für Ernährungsforschung, Potsdam Rehbrücke, and German Center for Diabetes Research (DZD), München-Neuherberg, 14558 Potsdam-Rehbrücke, Germany
| | - Ilka Wilhelmi
- Deutsches Institut für Ernährungsforschung, Potsdam Rehbrücke, and German Center for Diabetes Research (DZD), München-Neuherberg, 14558 Potsdam-Rehbrücke, Germany
| | - Oliver Daumke
- Max-Delmbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany
| | - Jan Schmoranzer
- Charité Universitätsmedizin Berlin, Advanced Medical Bioimaging Core Facility - AMBIO, 10117 Berlin, Germany
| | - Annette Schürmann
- Deutsches Institut für Ernährungsforschung, Potsdam Rehbrücke, and German Center for Diabetes Research (DZD), München-Neuherberg, 14558 Potsdam-Rehbrücke, Germany
| | - Michael Krauss
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Berlin, Molecular Pharmacology and Cell Biology, 13125 Berlin, Germany
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Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol 2017; 13:922. [PMID: 28348067 PMCID: PMC5371729 DOI: 10.15252/msb.20167062] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.
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Affiliation(s)
- Pierre M Jean Beltran
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
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