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Proteomes
Special Issues
Proteomic Analysis of Host-Microbial Pathogen Interactions
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Proteomic Analysis of Host-Microbial Pathogen Interactions

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (1 March 2018) | Viewed by 20594

Special Issue Editors

Prof. Dr. Rembert Pieper

E-Mail Website
Guest Editor
Adjunct Scientist, J Craig Venter Institute, Rockville, MD, USA
Interests: host-pathogen interactions; biomarkers; systems biology; biochemistry; proteomics
Dr. Yanbao Yu

E-Mail Website
Guest Editor
J. Craig Venter Institute, Rockville, MD, USA
Interests: quantitative proteomics; clinical proteomics; LC-MS/MS; label-free quantitation; SILAC/iTRAQ; affinity purification mass spec (AP-MS); protein modifications characterization (PTMs); signaling network analysis in innate immunity; host-pathogen interactions; human microbiome; metaproteomics; biomarker discovery; sample preparation; HPLC fractionation

Special Issue Information

Dear Colleagues,

In the last decade, proteomic technologies and the associated computational analysis methods have advanced to a level that not only permits studies on the interrogation of host-pathogen interactions using model systems (e.g., cell co-cultures) but also clinical samples. I encourage contributions associated with various infectious diseases, the use of different technologies (e.g., mass spectrometry-based proteomics, protein arrays and antibody arrays), different pathogens (e.g., bacteria, fungi and protozoa), different hosts (human, animals and plants), co-infections with viral/bacterial pathogens and host-pathogen interactions in the context of a resident microbiome. Contributions may also focus on infectious disease diagnosis, the antimicrobial treatment and antibiotic resistance of a pathogen if the host environment is a component of the research. Furthermore, articles related to technical advances in proteomics that facilitate the study of host-pathogen interactions are welcome.

Proteomic research on host-pathogen interactions can drive the discovery of novel therapeutic targets for infectious diseases, discover new mechanisms of pathogenesis, unravel the complexity of an infectious disease and, in the context of mammalian hosts, characterize the immune response towards an invading pathogen. Proteomic research can provide critical insights into the communications of more than one microbial species, including those that do not harm the host, with the host environment. This is an exciting time to push this technology further into the limelight of host-pathogen interaction research and to demonstrate its important role in infectious disease systems biology.

We look forward to receiving your manuscripts.

Prof. Dr. Rembert Pieper
Dr. Yanbao Yu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial proteome

  • pathogen proteome

  • inflammation

  • immune defense

  • immune proteomics

  • virulence factor

  • pathogenesis

  • pathogen

  • inter-microbial communication

  • microbial colonization

  • intracellular pathogen

  • microbial biofilm

  • bacterial biofilm

  • infection

  • bacterial adhesion

  • bacterial invasion

  • host-pathogen interactions

  • microbial identification

  • cell surface protein modification

  • fungal pathogen

  • pathogen adaptation to host environment

  • pathogen adaptation to immune defenses

Published Papers (4 papers)

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Research

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18 pages, 1329 KiB  
Article
Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms
by Yanbao Yu, Tamara Tsitrin, Harinder Singh, Sebastian N. Doerfert, Maria V. Sizova, Slava S. Epstein and Rembert Pieper
Proteomes 2018, 6(4), 52; https://doi.org/10.3390/proteomes6040052 - 09 Dec 2018
Cited by 5 | Viewed by 5040
Abstract
Actinobaculum massiliense, a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored more common uropathogens, such as Proteus mirabilis [...] Read more.
Actinobaculum massiliense, a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored more common uropathogens, such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense is adapted to a life style in polymicrobial biofilms. We isolated a clinical strain from a blood agar colony and used 16S rRNA gene sequencing and shotgun proteomics to confirm its identity as A. massiliense. We characterized this species by quantitatively comparing the bacterial proteome derived from in vitro growth with that of four clinical samples. The functional relevance of proteins with emphasis on nutrient import and the response to hostile host conditions, showing evidence of neutrophil infiltration, was analyzed. Two putative subtilisin-like proteases and a heme/oligopeptide transporter were abundant in vivo and are likely important for survival and fitness in the biofilm. Proteins facilitating uptake of xylose/glucuronate and oligopeptides, also highly expressed in vivo, may feed metabolites into mixed acid fermentation and peptidolysis pathways, respectively, to generate energy. A polyketide synthase predicted to generate a secondary metabolite that interacts with either the human host or co-colonizing microbes was also identified. The product of the PKS enzyme may contribute to A. massiliense fitness and persistence in the CBs. Full article
(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)
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1871 KiB  
Article
Isolation and Characterization of Serum Extracellular Vesicles (EVs) from Atlantic Salmon Infected with Piscirickettsia Salmonis
by Leidy Lagos, Julia Tandberg, Alexander Kashulin-Bekkelund, Duncan J. Colquhoun, Henning Sørum and Hanne C. Winther-Larsen
Proteomes 2017, 5(4), 34; https://doi.org/10.3390/proteomes5040034 - 01 Dec 2017
Cited by 19 | Viewed by 4153
Abstract
Secretion of extracellular vesicles (EVs) is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is [...] Read more.
Secretion of extracellular vesicles (EVs) is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is known, however, of EV secretion in fish, or the effect of infection on EV release and content. In the present study, EVs were isolated from the serum of healthy and Piscirickettsia salmonis infected Atlantic salmon in order to evaluate the effect of infection on EV secretion. P. salmonis is facultative intracellular bacterium that causes a systemic infection disease in farmed salmonids. EVs isolated from both infected and non-infected fish had an average diameter of 230–300 nm, as confirmed by transmission electron microscopy, nanoparticle tracking, and flow cytometry. Mass spectrometry identified 180 proteins in serum EVs from both groups of fish. Interestingly, 35 unique proteins were identified in serum EVs isolated from the fish infected with P. salmonis. These unique proteins included proteasomes subunits, granulins, and major histocompatibility class I and II. Our results suggest that EV release could be part of a mechanism in which host stimulatory molecules are released from infected cells to promote an immune response. Full article
(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)
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5488 KiB  
Article
Interaction of Recombinant Gallus gallus SEPT5 and Brain Proteins of H5N1-Avian Influenza Virus-Infected Chickens
by Jasmine Elanie Khairat, Vinod Balasubramaniam, Iekhsan Othman, Abdul Rahman Omar and Sharifah Syed Hassan
Proteomes 2017, 5(3), 23; https://doi.org/10.3390/proteomes5030023 - 12 Sep 2017
Cited by 6 | Viewed by 4789
Abstract
Septin forms a conserved family of cytoskeletal guanosine triphosphate (GTP) binding proteins that have diverse roles in protein scaffolding, vesicle trafficking, and cytokinesis. The involvement of septins in infectious viral disease pathogenesis has been demonstrated by the upregulation of SEPT5 protein and its [...] Read more.
Septin forms a conserved family of cytoskeletal guanosine triphosphate (GTP) binding proteins that have diverse roles in protein scaffolding, vesicle trafficking, and cytokinesis. The involvement of septins in infectious viral disease pathogenesis has been demonstrated by the upregulation of SEPT5 protein and its mRNA in brain tissues of H5N1-infected chickens, thus, providing evidence for the potential importance of this protein in the pathogenesis of neurovirulence caused by the avian influenza virus. In this study, cloning, expression, and purification of Gallus gallus SEPT5 protein was performed in Escherichia coli. The SEPT5 gene was inserted into the pRSETB expression vector, transformed in the E. coli BL21 (DE3) strain and the expression of SEPT5 protein was induced by IPTG. The SEPT5 protein was shown to be authentic as it was able to be pulled down by a commercial anti-SEPT5 antibody in a co-immunoprecipitation assay. In vivo aggregation of the recombinant protein was limited by cultivation at a reduced temperature of 16 °C. Using co-immunoprecipitation techniques, the purified recombinant SEPT5 protein was used to pull down host’s interacting or binding proteins, i.e., proteins of brains of chickens infected with the H5N1 influenza virus. Interacting proteins, such as CRMP2, tubulin proteins, heat-shock proteins and other classes of septins were identified using LCMS/MS. Results from this study suggest that the codon-optimized SEPT5 gene can be efficiently expressed in the E. coli bacterial system producing authentic SEPT5 protein, thus, enabling multiple host’s proteins to interact with the SEPT5 protein. Full article
(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)
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Review

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2008 KiB  
Review
Proteogenomics in Aid of Host–Pathogen Interaction Studies: A Bacterial Perspective
by Ursula Fels, Kris Gevaert and Petra Van Damme
Proteomes 2017, 5(4), 26; https://doi.org/10.3390/proteomes5040026 - 11 Oct 2017
Cited by 14 | Viewed by 6037
Abstract
By providing useful tools to study host–pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, [...] Read more.
By providing useful tools to study host–pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of proteogenomics approaches to study bacterial pathogenesis. In addition, we review different omics strategies (i.e., transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host. Full article
(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)
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