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Proteomic Analysis of Microorganisms

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 24759

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Special Issue Editors

Prof. Dr. Seung Il Kim

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Guest Editor

1. Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Korea
2. Department of Bio-analysis Science, University of Science and Technology (UST), Daejeon, Korea
Interests: proteomics of infectious disease (major pathogens: Acinetobacter baumannii, Streptococcus pneumonia, Orientia tsutsugamushi, SFTS et al); characterization of extracelluar vesicles of pathogenic bacteria; screening and development of protein biomarkers for pathogenic bacteria and virus; urine and serum proteomics of infectious disease

Mr. Hayoung Lee

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Assistant Guest Editor

Research center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Cheongju 28119, Korea
Interests: infectious disease; bioinformatics; proteomics and biomarker

Special Issue Information

Dear Colleagues,

Microorganisms are useful samples for the development of new omics technologies, including proteomics, because of their simple genomic size. Despite the complementary role of proteomics, this technology is an essential tool for explaining PTM (post-translational modification), secreted proteins, membrane proteins, extracellular vesicles, diagnostic protein makers, and more. In general, microorganisms have versatile abilities that allow them to adapt to familiar culture conditions in harsh environments. A proteomic analysis of microorganisms still provides useful information for its role in a unique ecological niche for basic and application research.

This Special Issue is made up of recent studies which focus on the proteomic analysis of microorganisms. These include: the proteomic characterization of a single microorganism or microbiomes under specific culture conditions, the characterization of novel secreted proteomes or extracellular vesicles (EV) of the microorganism for screening of biomarkers; the application of proteomic tools to elucidate the mechanism of specific physiological characterization of microorganisms; the proteomic analysis of clinical samples from human patients involved with infectious diseases or animal models; other proteomic results related to the environmental or pathogenic microorganisms and viruses.

Prof. Dr. Seung Il Kim
Guest Editor
Mr. Hayoung Lee
Assistant Guest Editor

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Keywords

MS/MS analysis
secreted proteome
diagnostic protein markers
quantititive proteome analysis
membrane proteomics
pathogenic bacteria
PTM
infectious diesase

Published Papers (10 papers)

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Editorial

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3 pages, 152 KiB

Open AccessEditorial

Proteomic Analysis of Microorganisms

by Seung Il Kim

Int. J. Mol. Sci. 2022, 23(8), 4329; https://doi.org/10.3390/ijms23084329 - 14 Apr 2022

Viewed by 1275

Abstract

At the early stage of the development of proteomic technologies, Escherichia coli or Saccharomyces cerevisiae were used as model microorganisms for high-throughput identification technologies, such as shotgun proteomics or 2D gel electrophoresis-based LC-MS/MS analysis [...] Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

Research

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17 pages, 1774 KiB

Open AccessArticle

Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi

by Alexander V. Shabaev, Konstantin V. Moiseenko, Olga A. Glazunova, Olga S. Savinova and Tatyana V. Fedorova

Int. J. Mol. Sci. 2022, 23(18), 10322; https://doi.org/10.3390/ijms231810322 - 07 Sep 2022

Cited by 7 | Viewed by 1479

Abstract

White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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17 pages, 5261 KiB

Open AccessArticle

Heme A Synthase Deficiency Affects the Ability of Bacillus cereus to Adapt to a Nutrient-Limited Environment

by Alice Chateau, Béatrice Alpha-Bazin, Jean Armengaud and Catherine Duport

Int. J. Mol. Sci. 2022, 23(3), 1033; https://doi.org/10.3390/ijms23031033 - 18 Jan 2022

Cited by 4 | Viewed by 2735

Abstract

The branched aerobic respiratory chain in Bacillus cereus comprises three terminal oxidases: cytochromes aa3, caa3, and bd. Cytochrome caa3 requires heme A for activity, which is produced from heme O by heme A synthase (CtaA). In this study, we deleted the ctaA gene in B. cereus AH187 strain, this deletion resulted in loss of cytochrome caa3 activity. Proteomics data indicated that B. cereus grown in glucose-containing medium compensates for the loss of cytochrome caa3 activity by remodeling its respiratory metabolism. This remodeling involves up-regulation of cytochrome aa3 and several proteins involved in redox stress response—to circumvent sub-optimal respiratory metabolism. CtaA deletion changed the surface-composition of B. cereus, affecting its motility, autoaggregation phenotype, and the kinetics of biofilm formation. Strikingly, proteome remodeling made the ctaA mutant more resistant to cold and exogenous oxidative stresses compared to its parent strain. Consequently, we hypothesized that ctaA inactivation could improve B. cereus fitness in a nutrient-limited environment. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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13 pages, 2124 KiB

Open AccessArticle

Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle

by Xiaoyin Zhang, Zhanbo Xiong, Ming Li, Nan Zheng, Shengguo Zhao and Jiaqi Wang

Int. J. Mol. Sci. 2022, 23(2), 817; https://doi.org/10.3390/ijms23020817 - 13 Jan 2022

Cited by 2 | Viewed by 1709

Abstract

Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema. Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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14 pages, 8653 KiB

Open AccessArticle

Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages

by Xueting Ma, Baohong Liu, Zhenxing Gong, Zigang Qu and Jianping Cai

Int. J. Mol. Sci. 2021, 22(22), 12110; https://doi.org/10.3390/ijms222212110 - 09 Nov 2021

Cited by 6 | Viewed by 2086

Abstract

Protein phosphorylation is an important post-translational modification (PTM) involved in diverse cellular functions. It is the most prevalent PTM in both Toxoplasma gondii and Plasmodium falciparum, but its status in Eimeria tenella has not been reported. Herein, we performed a comprehensive, quantitative phosphoproteomic profile analysis of four stages of the E. tenella life cycle: unsporulated oocysts (USO), partially sporulated (7 h) oocysts (SO7h), sporulated oocysts (SO), and sporozoites (S). A total of 15,247 phosphorylation sites on 9514 phosphopeptides corresponding to 2897 phosphoproteins were identified across the four stages. In addition, 456, 479, and 198 differentially expressed phosphoproteins (DEPPs) were identified in the comparisons SO7h vs. USO, SO vs. SO7h, and S vs. SO, respectively. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEPPs suggested that they were involved in diverse functions. For SO7h vs. USO, DEPPs were mainly involved in cell division, actin cytoskeleton organization, positive regulation of transport, and pyruvate metabolism. For SO vs. SO7h, they were related to the peptide metabolic process, translation, and RNA transport. DEPPs in the S vs. SO comparison were associated with the tricarboxylic acid metabolic process, positive regulation of ATPase activity, and calcium ion binding. Time course sequencing data analysis (TCseq) identified six clusters with similar expression change characteristics related to carbohydrate metabolism, cytoskeleton organization, and calcium ion transport, demonstrating different regulatory profiles across the life cycle of E. tenella. The results revealed significant changes in the abundance of phosphoproteins during E. tenella development. The findings shed light on the key roles of protein phosphorylation and dephosphorylation in the E. tenella life cycle. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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18 pages, 2577 KiB

Open AccessArticle

Exoproteome Analysis of Antagonistic Interactions between the Probiotic Bacteria Limosilactobacillus reuteri LR1 and Lacticaseibacillus rhamnosus F and Multidrug Resistant Strain of Klebsiella pneumonia

by Olga S. Savinova, Olga A. Glazunova, Konstantin V. Moiseenko, Anna V. Begunova, Irina V. Rozhkova and Tatyana V. Fedorova

Int. J. Mol. Sci. 2021, 22(20), 10999; https://doi.org/10.3390/ijms222010999 - 12 Oct 2021

Cited by 11 | Viewed by 2213

Abstract

The expansion of multiple drug resistant (MDR) strains of Klebsiella pneumoniae presents an immense threat for public health. Annually, this microorganism causes thousands of lethal nosocomial infections worldwide. Currently, it has been shown that certain strains of lactic acid bacteria (LAB) can efficiently inhibit growth of K. pneumoniae and the formation of its biofilms; however, the active principle of such action remains unknown. In the current article, the growth inhibition of MDR K. pneumoniae by two LAB—Limosilactobacillus reuteri LR1 and Lacticaseibacillus rhamnosus F—is demonstrated, and the nature of this inhibition studied at the level of exoproteome. This article shows that the exoproteomes of studied LAB contains both classically and non-classically secreted proteins. While for L. reuteri LR1 the substantial portion of classically secreted proteins was presented by cell-wall-degrading enzymes, for L. rhamnosus F only one out of four classically secreted proteins was presented by cell-wall hydrolase. Non-classically secreted proteins of both LAB were primarily metabolic enzymes, for some of which a possible moonlighting functioning was proposed. These results contribute to knowledge regarding antagonistic interaction between LAB and pathogenic and opportunistic microorganisms and set new perspectives for the use of LAB to control the spread of these microorganisms. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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18 pages, 1953 KiB

Open AccessArticle

Cysteine Proteome Reveals Response to Endogenous Oxidative Stress in Bacillus cereus

by Fella Hamitouche, Jean Armengaud, Luc Dedieu and Catherine Duport

Int. J. Mol. Sci. 2021, 22(14), 7550; https://doi.org/10.3390/ijms22147550 - 14 Jul 2021

Cited by 6 | Viewed by 2116

Abstract

At the end of exponential growth, aerobic bacteria have to cope with the accumulation of endogenous reactive oxygen species (ROS). One of the main targets of these ROS is cysteine residues in proteins. This study uses liquid chromatography coupled to high-resolution tandem mass spectrometry to detect significant changes in protein abundance and thiol status for cysteine-containing proteins from Bacillus cereus during aerobic exponential growth. The proteomic profiles of cultures at early-, middle-, and late-exponential growth phases reveals that (i) enrichment in proteins dedicated to fighting ROS as growth progressed, (ii) a decrease in both overall proteome cysteine content and thiol proteome redox status, and (iii) changes to the reduced thiol status of some key proteins, such as the transition state transcriptional regulator AbrB. Taken together, our data indicate that growth under oxic conditions requires increased allocation of protein resources to attenuate the negative effects of ROS. Our data also provide a strong basis to understand the response mechanisms used by B. cereus to deal with endogenous oxidative stress. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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20 pages, 9171 KiB

Open AccessArticle

Biophysical and Biochemical Comparison of Extracellular Vesicles Produced by Infective and Non-Infective Stages of Trypanosoma cruzi

by Lissette Retana Moreira, Alexa Prescilla-Ledezma, Alberto Cornet-Gomez, Fátima Linares, Ana Belén Jódar-Reyes, Jorge Fernandez, Ana Karina Ibarrola Vannucci, Luis Miguel De Pablos and Antonio Osuna

Int. J. Mol. Sci. 2021, 22(10), 5183; https://doi.org/10.3390/ijms22105183 - 13 May 2021

Cited by 19 | Viewed by 3317

Abstract

Extracellular vesicles (EVs) are small lipid vesicles released by either any prokaryotic or eukaryotic cell, or both, with a biological role in cell-to-cell communication. In this work, we characterize the proteomes and nanomechanical properties of EVs released by tissue-culture cell-derived trypomastigotes (mammalian infective stage; (TCT)) and epimastigotes (insect stage; (E)) of Trypanosoma cruzi, the etiologic agent of Chagas disease. EVs of each stage were isolated by differential centrifugation and analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS), dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), electron microscopy and atomic force microscopy (AFM). Measurements of zeta-potential were also included. Results show marked differences in the surface molecular cargos of EVs between both stages, with a noteworthy expansion of all groups of trans-sialidase proteins in trypomastigote’s EVs. In contrast, chromosomal locations of trans-sialidases of EVs of epimastigotes were dramatically reduced and restricted to subtelomeric regions, indicating a possible regulatable expression of these proteins between both stages of the parasite. Regarding mechanical properties, EVs of trypomastigotes showed higher adhesion compared to the EVs of epimastigotes. These findings demonstrate the remarkable surface remodeling throughout the life cycle of T. cruzi, which shapes the physicochemical composition of the extracellular vesicles and could have an impact in the ability of these vesicles to participate in cell communication in completely different niches of infection. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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23 pages, 6625 KiB

Open AccessArticle

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis

by Anton E. Shikov, Yury V. Malovichko, Arseniy A. Lobov, Maria E. Belousova, Anton A. Nizhnikov and Kirill S. Antonets

Int. J. Mol. Sci. 2021, 22(5), 2244; https://doi.org/10.3390/ijms22052244 - 24 Feb 2021

Cited by 5 | Viewed by 2798

Abstract

Bacillus thuringiensis, commonly referred to as Bt, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make Bt a prominent source of biologicals. To categorize the exuberance of Bt strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of Bt strains’ phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in Bt strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of Bt culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the israelensis-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the israelensis strain were also compared to the spores of strains belonging to two other major Bt serovars, namely darmstadiensis and thuringiensis. The identified proteins were analyzed regarding the presence of the respective genes in the 104 Bt genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains’ phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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Review

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21 pages, 5698 KiB

Open AccessReview

Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases

by Hayoung Lee and Seung Il Kim

Int. J. Mol. Sci. 2022, 23(4), 2187; https://doi.org/10.3390/ijms23042187 - 16 Feb 2022

Cited by 6 | Viewed by 3855

Abstract

Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography–mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed. Full article

(This article belongs to the Special Issue Proteomic Analysis of Microorganisms)

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