Special Issue "Microbial Proteomics"

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

Deadline for manuscript submissions: closed (31 August 2015)

Special Issue Editors

Guest Editor
Prof. Dr. Michael Hecker

Institute of Microbiology, Ernst Moritz Arndt University Greifswald, F.-L.-Jahn-Straße 15, D-17487 Greifswald, Germany
Website | E-Mail
Fax: +49 3834 864202
Interests: microbial physiology; stress and starvation response of bacteria; physiological proteomics of bacteria; proteomic view of pathogenicity of bacteria (Staphylococcus aureus etc.)
Guest Editor
Prof. Dr. Katharina Riedel

Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany
Website | E-Mail
Interests: microbial proteomics; metaproteomics; environmental proteomics; microbial biofilms; quorum sensing; Pseudomonas aeruginosa; Burkholderia sp.

Special Issue Information

Dear Colleagues,

State-of-the-art functional genomics technologies provide a panoramic view of microbial physiology and of the complex molecular interactions between microbes and their hosts. In particular, proteomics, by focusing on proteins as the “workhorses” of life, has revolutionized our perception of microbes by providing comprehensive qualitative and quantitative information on the protein composition of single cells, and on entire ecosystems. Consequently, proteomics has become an indispensable tool in microbiology for investigating central research topics ranging from global analyses of microbial physiology to investigations of the molecular interactions between commensal and pathogenic microbes and their hosts.

This Special Issue will outline the latest highlights of microbial proteomics research, and will also document the still existing challenges, together with innovative strategies suited to overcome methodological drawbacks. We will review current studies in medical, environmental, and applied microbiology employing proteomics to generate essential knowledge on the multi-layered network constituting microbial life between genome and environment, and thereby complementing hypothesis-driven, targeted research strategies.

Prof. Dr. Michael Hecker
Prof. Dr. Katharina Riedel
Guest Editors

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 papers will be 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 550 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 proteomics
  • sub-cellular proteomics
  • absolute protein quantification
  • immunoproteomics
  • in vivo proteomics & metaproteomics
  • bacterial physiology and stress response
  • global regulators
  • molecular mechanisms of microbial pathogenicity
  • host-pathogen interactions
  • plant-microbe interactions
  • human microbiome
  • structure & function of microbial communities
  • proteome-guided optimization of production strains

Related Special Issue

Published Papers (8 papers)

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Research

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Open AccessArticle A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades
Received: 24 September 2015 / Revised: 31 January 2016 / Accepted: 5 February 2016 / Published: 19 February 2016
Cited by 2 | PDF Full-text (4712 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Staphylococcus aureus is an important model organism and pathogen. This S. aureus proteome overview details shared and specific proteins and selected virulence-relevant protein complexes from representative strains of all three major clades. To determine the strain distribution and major clades we used a [...] Read more.
Staphylococcus aureus is an important model organism and pathogen. This S. aureus proteome overview details shared and specific proteins and selected virulence-relevant protein complexes from representative strains of all three major clades. To determine the strain distribution and major clades we used a refined strain comparison combining ribosomal RNA, MLST markers, and looking at highly-conserved regions shared between strains. This analysis shows three sub-clades (A–C) for S. aureus. As calculations are complex and strain annotation is quite time consuming we compare here key representatives of each clade with each other: model strains COL, USA300, Newman, and HG001 (clade A), model strain N315 and Mu50 (clade B) and ED133 and MRSA252 (clade C). We look at these individual proteomes and compare them to a background of 64 S. aureus strains. There are overall 13,284 S. aureus proteins not part of the core proteome which are involved in different strain-specific or more general complexes requiring detailed annotation and new experimental data to be accurately delineated. By comparison of the eight representative strains, we identify strain-specific proteins (e.g., 18 in COL, 105 in N315 and 44 in Newman) that characterize each strain and analyze pathogenicity islands if they contain such strain-specific proteins. We identify strain-specific protein repertoires involved in virulence, in cell wall metabolism, and phosphorylation. Finally we compare and analyze protein complexes conserved and well-characterized among S. aureus (a total of 103 complexes), as well as predict and analyze several individual protein complexes, including structure modeling in the three clades. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessArticle P40 and P90 from Mpn142 are Targets of Multiple Processing Events on the Surface of Mycoplasma pneumoniae
Proteomes 2015, 3(4), 512-537; https://doi.org/10.3390/proteomes3040512
Received: 20 September 2015 / Revised: 2 December 2015 / Accepted: 7 December 2015 / Published: 16 December 2015
Cited by 5 | PDF Full-text (1895 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Mycoplasma pneumoniae is a significant cause of community acquired pneumonia globally. Despite having a genome less than 1 Mb in size, M. pneumoniae presents a structurally sophisticated attachment organelle that (i) provides cell polarity, (ii) directs adherence to receptors presented on respiratory epithelium, [...] Read more.
Mycoplasma pneumoniae is a significant cause of community acquired pneumonia globally. Despite having a genome less than 1 Mb in size, M. pneumoniae presents a structurally sophisticated attachment organelle that (i) provides cell polarity, (ii) directs adherence to receptors presented on respiratory epithelium, and (iii) plays a major role in cell motility. The major adhesins, P1 (Mpn141) and P30 (Mpn453), are localised to the tip of the attachment organelle by the surface accessible cleavage fragments P90 and P40 derived from Mpn142. Two events play a defining role in the formation of P90 and P40; removal of a leader peptide at position 26 (23SLA↓NTY28) during secretion to the cell surface and cleavage at amino acid 455 (452GPL↓RAG457) generating P40 and P90. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis of tryptic peptides generated by digesting size-fractionated cell lysates of M. pneumoniae identified 15 cleavage fragments of Mpn142 ranging in mass from 9–84 kDa. Further evidence for the existence of cleavage fragments of Mpn142 was generated by mapping tryptic peptides to proteins recovered from size fractionated eluents from affinity columns loaded with heparin, fibronectin, fetuin, actin, plasminogen and A549 surface proteins as bait. To define the sites of cleavage in Mpn142, neo-N-termini in cell lysates of M. pneumoniae were dimethyl-labelled and characterised by LC-MS/MS. Our data suggests that Mpn142 is cleaved to generate adhesins that are auxiliary to P1 and P30. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessArticle A Proteomic Study of Clavibacter Michiganensis Subsp. Michiganensis Culture Supernatants
Proteomes 2015, 3(4), 411-423; https://doi.org/10.3390/proteomes3040411
Received: 14 August 2015 / Revised: 30 October 2015 / Accepted: 10 November 2015 / Published: 12 November 2015
Cited by 3 | PDF Full-text (1188 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Clavibacter michiganensis, subsp. michiganensis is a Gram-positive plant pathogen infecting tomato (Solanum lycopersicum). Despite a considerable economic importance due to significant losses of infected plants and fruits, knowledge about virulence factors of C. michiganensis subsp. michiganensis and host-pathogen interactions on [...] Read more.
Clavibacter michiganensis, subsp. michiganensis is a Gram-positive plant pathogen infecting tomato (Solanum lycopersicum). Despite a considerable economic importance due to significant losses of infected plants and fruits, knowledge about virulence factors of C. michiganensis subsp. michiganensis and host-pathogen interactions on a molecular level are rather limited. In the study presented here, the proteome of culture supernatants from C. michiganensis subsp. michiganensis NCPPB382 was analyzed. In total, 1872 proteins were identified in M9 and 1766 proteins in xylem mimicking medium. Filtration of supernatants before protein precipitation reduced these to 1276 proteins in M9 and 976 proteins in the xylem mimicking medium culture filtrate. The results obtained indicate that C. michiganensis subsp. michiganensis reacts to a sucrose- and glucose-depleted medium similar to the xylem sap by utilizing amino acids and host cell polymers as well as their degradation products, mainly peptides, amino acids and various C5 and C6 sugars. Interestingly, the bacterium expresses the previously described virulence factors Pat-1 and CelA not exclusively after host cell contact in planta but already in M9 minimal and xylem mimicking medium. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessArticle The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus
Proteomes 2015, 3(4), 347-368; https://doi.org/10.3390/proteomes3040347
Received: 31 August 2015 / Revised: 15 October 2015 / Accepted: 19 October 2015 / Published: 27 October 2015
Cited by 3 | PDF Full-text (1751 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The growth and productivity of ruminants depends on a complex microbial community found in their fore-stomach (rumen), which is able to breakdown plant polysaccharides and ferment the released sugars. Butyrivibrio proteoclasticus B316T is a Gram-positive polysaccharide-degrading, butyrate-producing bacterium that is present at high [...] Read more.
The growth and productivity of ruminants depends on a complex microbial community found in their fore-stomach (rumen), which is able to breakdown plant polysaccharides and ferment the released sugars. Butyrivibrio proteoclasticus B316T is a Gram-positive polysaccharide-degrading, butyrate-producing bacterium that is present at high numbers in the rumen of animals consuming pasture or grass silage based diets. B316T is one of a small number of rumen fibrolytic microbes capable of efficiently degrading and utilizing xylan, as well as being capable of utilizing arabinose, xylose, pectin and starch. We have therefore carried out a proteomic analysis of B316T to identify intracellular enzymes that are implicated in the metabolism of internalized xylan. Three hundred and ninety four proteins were identified including enzymes that have potential to metabolize assimilated products of extracellular xylan digestion. Identified enzymes included arabinosidases, esterases, an endoxylanase, and β-xylosidase. The presence of intracellular debranching enzymes indicated that some hemicellulosic side-chains may not be removed until oligosaccharides liberated by extracellular digestion have been assimilated by the cells. The results support a model of extracellular digestion of hemicellulose to oligosaccharides that are then transported to the cytoplasm for further digestion by intracellular enzymes. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Review

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Open AccessReview Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates
Received: 3 November 2015 / Revised: 5 February 2016 / Accepted: 1 March 2016 / Published: 7 March 2016
Cited by 7 | PDF Full-text (986 KB) | HTML Full-text | XML Full-text
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of [...] Read more.
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessReview Proteomics in the Study of Bacterial Keratitis
Proteomes 2015, 3(4), 496-511; https://doi.org/10.3390/proteomes3040496
Received: 5 August 2015 / Revised: 13 November 2015 / Accepted: 7 December 2015 / Published: 14 December 2015
Cited by 2 | PDF Full-text (766 KB) | HTML Full-text | XML Full-text
Abstract
Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial [...] Read more.
Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial keratitis can progress rapidly, leading to corneal destruction and potential blindness. Common risk factors for bacterial keratitis include contact lens wear, ocular trauma, ocular surface disease, ocular surgery, lid deformity, chronic use of topical steroids, contaminated ocular medications or solutions, and systemic immunosuppression. The pathogenesis of bacterial keratitis, which depends on the bacterium-host interaction and the virulence of the invading bacterium, is complicated and not completely understood. This review highlights some of the proteomic technologies that have been used to identify virulence factors and the host response to infections of bacterial keratitis in order to understand the disease process and develop improved methods of diagnosis and treatment. Although work in this field is not abundant, proteomic technologies have provided valuable information toward our current knowledge of bacterial keratitis. More studies using global proteomic approaches are warranted because it is an important tool to identify novel targets for intervention and prevention of corneal damage caused by these virulent microorganisms. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessReview Challenges and Strategies for Proteome Analysis of the Interaction of Human Pathogenic Fungi with Host Immune Cells
Proteomes 2015, 3(4), 467-495; https://doi.org/10.3390/proteomes3040467
Received: 9 September 2015 / Revised: 23 November 2015 / Accepted: 8 December 2015 / Published: 14 December 2015
Cited by 2 | PDF Full-text (1694 KB) | HTML Full-text | XML Full-text
Abstract
Opportunistic human pathogenic fungi including the saprotrophic mold Aspergillus fumigatus and the human commensal Candida albicans can cause severe fungal infections in immunocompromised or critically ill patients. The first line of defense against opportunistic fungal pathogens is the innate immune system. Phagocytes such [...] Read more.
Opportunistic human pathogenic fungi including the saprotrophic mold Aspergillus fumigatus and the human commensal Candida albicans can cause severe fungal infections in immunocompromised or critically ill patients. The first line of defense against opportunistic fungal pathogens is the innate immune system. Phagocytes such as macrophages, neutrophils and dendritic cells are an important pillar of the innate immune response and have evolved versatile defense strategies against microbial pathogens. On the other hand, human-pathogenic fungi have sophisticated virulence strategies to counteract the innate immune defense. In this context, proteomic approaches can provide deeper insights into the molecular mechanisms of the interaction of host immune cells with fungal pathogens. This is crucial for the identification of both diagnostic biomarkers for fungal infections and therapeutic targets. Studying host-fungal interactions at the protein level is a challenging endeavor, yet there are few studies that have been undertaken. This review draws attention to proteomic techniques and their application to fungal pathogens and to challenges, difficulties, and limitations that may arise in the course of simultaneous dual proteome analysis of host immune cells interacting with diverse morphotypes of fungal pathogens. On this basis, we discuss strategies to overcome these multifaceted experimental and analytical challenges including the viability of immune cells during co-cultivation, the increased and heterogeneous protein complexity of the host proteome dynamically interacting with the fungal proteome, and the demands on normalization strategies in terms of relative quantitative proteome analysis. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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Open AccessReview Microbial Metalloproteomics
Proteomes 2015, 3(4), 424-439; https://doi.org/10.3390/proteomes3040424
Received: 1 September 2015 / Revised: 4 November 2015 / Accepted: 23 November 2015 / Published: 1 December 2015
Cited by 2 | PDF Full-text (1633 KB) | HTML Full-text | XML Full-text
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized [...] Read more.
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas. Full article
(This article belongs to the Special Issue Microbial Proteomics)
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