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Proteomes
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Microbial Proteomics II
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Microbial Proteomics II

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

Deadline for manuscript submissions: closed (31 July 2020) | Viewed by 36002

Special Issue Editors

Assoc. Prof. Ansgar Poetsch

E-Mail Website
Guest Editor
School of Biomedical and Healthcare Scienes, University of Plymouth, Plymouth, United Kingdom; Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
Interests: protein turnover; membrane proteins; biotechnology; systems biology; proteases; microbial population heterogeneity
Prof. Dr. Andreas Burkovski

E-Mail Website
Guest Editor
Microbiology Division, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
Interests: corynebacteria; host–pathogen interaction; nitrogen control; regulatory networks; secretome analyses; toxins
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As a global analysis technique, proteomics has become to an invaluable tool for the characterization of microbial processes from general physiology; biomedical and biotechnological aspects of individual bacteria, extending to interactions between commensal and pathogenic bacteria; and their respective host organisms, in the last two decades. This Special Issue will give an overview on the current status of microbial proteomics, but aims also to review recent highlights and challenges.

Assoc. Prof. Ansgar Poetsch
Prof. Andreas Burkovski
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 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

  • absolute protein quantification
  • bacterial physiology and stress response
  • host–pathogen interactions
  • human microbiome
  • immunoproteomics
  • metaproteomics
  • microbial pathogenicity
  • microbial proteomics
  • plant–microbe interactions
  • protein modifications
  • proteogenomics
  • regulatory networks
  • systems biology

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Related Special Issue

Published Papers (6 papers)

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Research

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17 pages, 1768 KiB  
Article
Short-Chain Fatty Acids Modulate Metabolic Pathways and Membrane Lipids in Prevotella bryantii B14
by Andrej Trautmann, Lena Schleicher, Simon Deusch, Jochem Gätgens, Julia Steuber and Jana Seifert
Proteomes 2020, 8(4), 28; https://doi.org/10.3390/proteomes8040028 - 16 Oct 2020
Cited by 23 | Viewed by 4707
Abstract
Short-chain fatty acids (SCFAs) are bacterial products that are known to be used as energy sources in eukaryotic hosts, whereas their role in the metabolism of intestinal microbes is rarely explored. In the present study, acetic, propionic, butyric, isobutyric, valeric, and isovaleric acid, [...] Read more.
Short-chain fatty acids (SCFAs) are bacterial products that are known to be used as energy sources in eukaryotic hosts, whereas their role in the metabolism of intestinal microbes is rarely explored. In the present study, acetic, propionic, butyric, isobutyric, valeric, and isovaleric acid, respectively, were added to a newly defined medium containing Prevotella bryantii B14 cells. After 8 h and 24 h, optical density, pH and SCFA concentrations were measured. Long-chain fatty acid (LCFA) profiles of the bacterial cells were analyzed via gas chromatography-time of flight-mass spectrometry (GC-ToF MS) and proteins were quantified using a mass spectrometry-based, label-free approach. Cultures supplemented with single SCFAs revealed different growth behavior. Structural features of the respective SCFAs were identified in the LCFA profiles, which suggests incorporation into the bacterial membranes. The proteomes of cultures supplemented with acetic and valeric acid differed by an increased abundance of outer membrane proteins. The proteome of the isovaleric acid supplementation showed an increase of proteins in the amino acid metabolism. Our findings indicate a possible interaction between SCFAs, the lipid membrane composition, the abundance of outer membrane proteins, and a modulation of branched chain amino acid biosynthesis by isovaleric acid. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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14 pages, 3008 KiB  
Article
Cellular and Extracellular Proteome of the Animal Pathogen Corynebacterium silvaticum, a Close Relative of Zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis
by Jens Möller, Svenja Schorlemmer, Jörg Hofmann and Andreas Burkovski
Proteomes 2020, 8(3), 19; https://doi.org/10.3390/proteomes8030019 - 12 Aug 2020
Cited by 9 | Viewed by 4507
Abstract
Corynebacterium silvaticum is a newly described animal pathogen, closely related to the emerging human pathogen Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, a major pathogen of small ruminants. In this study, proteins of a whole cell and a shaving fraction and the exoproteome of [...] Read more.
Corynebacterium silvaticum is a newly described animal pathogen, closely related to the emerging human pathogen Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, a major pathogen of small ruminants. In this study, proteins of a whole cell and a shaving fraction and the exoproteome of C. silvaticum strain W25 were analyzed as a first proteome study of this species. In total, 1305 proteins were identified out of 2013 proteins encoded by the W25 genome sequence and number of putative virulence factors were detected already under standard growth conditions including phospholipase D and sialidase. An up to now uncharacterized trypsin-like protease is by far the most secreted protein in this species, indicating a putative role in pathogenicity. Furthermore, the proteome analyses carried out in this study support the recently published taxonomical delineation of C. silvaticum from the closely related zoonotic Corynebacterium species. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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11 pages, 3145 KiB  
Article
A Preliminary Metagenome Analysis Based on a Combination of Protein Domains
by Yoji Igarashi, Daisuke Mori, Susumu Mitsuyama, Kazutoshi Yoshitake, Hiroaki Ono, Tsuyoshi Watanabe, Yukiko Taniuchi, Tomoko Sakami, Akira Kuwata, Takanori Kobayashi, Yoshizumi Ishino, Shugo Watabe, Takashi Gojobori and Shuichi Asakawa
Proteomes 2019, 7(2), 19; https://doi.org/10.3390/proteomes7020019 - 29 Apr 2019
Viewed by 4384
Abstract
Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have [...] Read more.
Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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11 pages, 2426 KiB  
Article
The Proteome of Tetrasphaera elongata is adapted to Changing Conditions in Wastewater Treatment Plants
by Florian-Alexander Herbst, Morten S. Dueholm, Reinhard Wimmer and Per Halkjær Nielsen
Proteomes 2019, 7(2), 16; https://doi.org/10.3390/proteomes7020016 - 25 Apr 2019
Cited by 22 | Viewed by 6304
Abstract
The activated sludge in wastewater treatment plants (WWTP) designed for enhanced biological phosphorus removal (EBPR) experiences periodically changing nutrient and oxygen availability. Tetrasphaera is the most abundant genus in Danish WWTP and represents up to 20–30% of the activated sludge community based on [...] Read more.
The activated sludge in wastewater treatment plants (WWTP) designed for enhanced biological phosphorus removal (EBPR) experiences periodically changing nutrient and oxygen availability. Tetrasphaera is the most abundant genus in Danish WWTP and represents up to 20–30% of the activated sludge community based on 16S rRNA amplicon sequencing and quantitative fluorescence in situ hybridization analyses, although the genus is in low abundance in the influent wastewater. Here we investigated how Tetrasphaera can successfully out-compete most other microorganisms in such highly dynamic ecosystems. To achieve this, we analyzed the physiological adaptations of the WWTP isolate T. elongata str. LP2 during an aerobic to anoxic shift by label-free quantitative proteomics and NMR-metabolomics. Escherichia coli was used as reference organism as it shares several metabolic capabilities and is regularly introduced to wastewater treatment plants without succeeding there. When compared to E. coli, only minor changes in the proteome of T. elongata were observed after the switch to anoxic conditions. This indicates that metabolic pathways for anaerobic energy harvest were already expressed during the aerobic growth. This allows continuous growth of Tetrasphaera immediately after the switch to anoxic conditions. Metabolomics furthermore revealed that the substrates provided were exploited far more efficiently by Tetrasphaera than by E. coli. These results suggest that T. elongata prospers in the dynamic WWTP environment due to adaptation to the changing environmental conditions. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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11 pages, 1518 KiB  
Article
More than a Toxin: Protein Inventory of Clostridium tetani Toxoid Vaccines
by Jens Möller, Max Edmund Kraner and Andreas Burkovski
Proteomes 2019, 7(2), 15; https://doi.org/10.3390/proteomes7020015 - 16 Apr 2019
Cited by 17 | Viewed by 7985
Abstract
Clostridium tetani is the etiological agent of tetanus, a life-threatening bacterial infection. The most efficient protection strategy against tetanus is a vaccination with the C. tetani neurotoxin, which is inactivated by formaldehyde-crosslinking. Since we assumed that besides the tetanus toxin, other proteins of [...] Read more.
Clostridium tetani is the etiological agent of tetanus, a life-threatening bacterial infection. The most efficient protection strategy against tetanus is a vaccination with the C. tetani neurotoxin, which is inactivated by formaldehyde-crosslinking. Since we assumed that besides the tetanus toxin, other proteins of C. tetani may also be present in toxoid preparations, we analyzed commercially available vaccines from different countries in respect to their protein content using mass spectrometry. In total 991 proteins could be identified in all five analyzed vaccines, 206 proteins were common in all analyzed vaccines and 54 proteins from the 206 proteins were potential antigens. The additionally present proteins may contribute at least partially to protection against C. tetani infection by supporting the function of the vaccine against the devastating effects of the tetanus toxin indirectly. Two different label-free protein quantification methods were applied for an estimation of protein contents. Similar results were obtained with a Total Protein Approach (TPA)-based method and Protein Discoverer 2.2 software package based on the minora algorithm. Depending on the tetanus toxoid vaccine and the quantification method used, tetanus neurotoxin contributes between 14 and 76 % to the total C. tetani protein content and varying numbers of other C. tetani proteins were detected. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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Review

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17 pages, 713 KiB  
Review
Proteomics of Brucella
by Ansgar Poetsch and María Inés Marchesini
Proteomes 2020, 8(2), 8; https://doi.org/10.3390/proteomes8020008 - 22 Apr 2020
Cited by 8 | Viewed by 6864
Abstract
Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the [...] Read more.
Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the molecular mechanisms underlying Brucella pathogenesis. Technological and methodological advancements such as increased instrument performance and multiplexed quantification have broadened the range of proteome studies, enabling new and improved analyses, providing deeper and more accurate proteome coverage. Indeed, proteomics has demonstrated its contribution to key research questions in Brucella biology, i.e., immunodominant proteins, host-cell interaction, stress response, antibiotic targets and resistance, protein secretion. Here, we review the proteomics of Brucella with a focus on more recent works and novel findings, ranging from reconfiguration of the intracellular bacterial proteome and studies on proteomic profiles of Brucella infected tissues, to the identification of Brucella extracellular proteins with putative roles in cell signaling and pathogenesis. In conclusion, proteomics has yielded copious new candidates and hypotheses that require future verification. It is expected that proteomics will continue to be an invaluable tool for Brucella and applications will further extend to the currently ill-explored aspects including, among others, protein processing and post-translational modification. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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