Статті в журналах: "Bacterial proteome"

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Tjalsma, Harold, Haike Antelmann, Jan D. H. Jongbloed, Peter G. Braun, Elise Darmon, Ronald Dorenbos, Jean-Yves F. Dubois, et al. "Proteomics of Protein Secretion by Bacillus subtilis: Separating the “Secrets” of the Secretome." Microbiology and Molecular Biology Reviews 68, no. 2 (June 2004): 207–33. http://dx.doi.org/10.1128/mmbr.68.2.207-233.2004.

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SUMMARY Secretory proteins perform a variety of important“ remote-control” functions for bacterial survival in the environment. The availability of complete genome sequences has allowed us to make predictions about the composition of bacterial machinery for protein secretion as well as the extracellular complement of bacterial proteomes. Recently, the power of proteomics was successfully employed to evaluate genome-based models of these so-called secretomes. Progress in this field is well illustrated by the proteomic analysis of protein secretion by the gram-positive bacterium Bacillus subtilis, for which ∼90 extracellular proteins were identified. Analysis of these proteins disclosed various“ secrets of the secretome,” such as the residence of cytoplasmic and predicted cell envelope proteins in the extracellular proteome. This showed that genome-based predictions reflect only∼ 50% of the actual composition of the extracellular proteome of B. subtilis. Importantly, proteomics allowed the first verification of the impact of individual secretion machinery components on the total flow of proteins from the cytoplasm to the extracellular environment. In conclusion, proteomics has yielded a variety of novel leads for the analysis of protein traffic in B. subtilis and other gram-positive bacteria. Ultimately, such leads will serve to increase our understanding of virulence factor biogenesis in gram-positive pathogens, which is likely to be of high medical relevance.

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Truong, Thuyen, Li Mei Pang, Suhasini Rajan, Sarah Sze Wah Wong, Yi Man Eva Fung, Lakshman Samaranayake, and Chaminda Jayampath Seneviratne. "The Proteome of Community Living Candida albicans Is Differentially Modulated by the Morphologic and Structural Features of the Bacterial Cohabitants." Microorganisms 8, no. 10 (October 7, 2020): 1541. http://dx.doi.org/10.3390/microorganisms8101541.

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Candida albicans is a commensal polymorphic and opportunistic fungus, which usually resides as a small community in the oral cavities of a majority of humans. The latter eco-system presents this yeast varied opportunities for mutualistic interactions with other cohabitant oral bacteria, that synergizes its persistence and pathogenicity. Collectively, these communities live within complex plaque biofilms which may adversely affect the oral health and increase the proclivity for oral candidiasis. The proteome of such oral biofilms with myriad interkingdom interactions are largely underexplored. Herein, we employed limma differential expression analysis, and cluster analysis to explore the proteomic interactions of C. albicans biofilms with nine different common oral bacterial species, Aggregatibacter actinomycetemcomitans, Actinomyces naeslundii, Fusobacterium nucleatum, Enterococcus faecalis, Porphyromonas gingivalis, Streptococcus mutants, Streptococcus sanguinis, Streptococcus mitis, and Streptococcus sobrinus. Interestingly, upon exposure of C. albicans biofilms to the foregoing heat-killed bacteria, the proteomes of the fungus associated with cellular respiration, translation, oxidoreductase activity, and ligase activity were significantly altered. Subsequent differential expression and cluster analysis revealed the subtle, yet significant alterations in the C. albicans proteome, particularly on exposure to bacteria with dissimilar cell morphologies, and Gram staining characteristics.

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Meng, Wenshu, Chenyang Zhao, and Youhe Gao. "Comparison of urine proteome among rat models by intraperitoneal injection with single bacteria and co-injection with two bacteria." PLOS ONE 16, no. 12 (December 31, 2021): e0261488. http://dx.doi.org/10.1371/journal.pone.0261488.

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Purpose To explore and compare urine proteome changes among rat models by intraperitoneal injection with single bacteria and co-injection with two bacteria. Method Escherichia coli and Staphylococcus aureus are two common human pathogens. Three rat models were established: (i) the intraperitoneal co-injection of E. coli and S. aureus model (ES model), (ii) intraperitoneal injection of E. coli model (E model), and (iii) intraperitoneal injection of S. aureus model (S model). Urinary proteomes on days 0, 1 and 2 of the three models were analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results A total of 111, 34 and 94 differential proteins were identified in the ES model, E model and S model, respectively. Among them, some differential proteins were reported to be associated with bacterial infection. Approximately 47% differential proteins in the E model overlapped with ES model, and 37% differential proteins in the S model overlapped with ES model. Compared with the E model and S model, a total of 71 unique differential proteins were identified in the ES model. Conclusion Our results indicated that (1) the urine proteome could distinguish different bacterial intraperitoneal injections models and (2) the effects of co-injection with two bacteria on the urine proteome were not simple superposition of single injection.

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Wang, Liang, Jianye Yang, Yaping Xu, Xue Piao, and Jichang Lv. "Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter." Current Genomics 20, no. 2 (May 22, 2019): 115–23. http://dx.doi.org/10.2174/1389202920666190320134438.

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Background: Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physiology and lifestyle. Objective: This study aims to understand how domains are distributed and duplicated in bacterial proteomes, in order to better understand bacterial physiology and lifestyles. Methods: In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference proteomes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In addition, the properties of no-domain proteins were investigated in terms of physicochemical properties. Results: The increasing number of non-redundant domains for a bacterial proteome follows the trend of an asymptotic function. The domain duplication rate is positively correlated with proteome size and increases more rapidly. The high percentage of single-domain proteins is more associated with small proteome size. For each proteome, unique domains were also obtained. Moreover, no-domain proteins show differences with the other three groups for several physicochemical properties analysed in this study. Conclusion: The study confirmed that a low domain duplication rate and a high percentage of singledomain proteins are more likely to be associated with bacterial host-dependent or restricted nicheadapted lifestyle. In addition, the unique lifestyle and physiology were revealed based on the analysis of species-specific domains and core domain interactions or co-occurrences.

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Fels, Ursula, Patrick Willems, Margaux De Meyer, Kris Gevaert, and Petra Van Damme. "Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective." PLOS Pathogens 19, no. 8 (August 3, 2023): e1011183. http://dx.doi.org/10.1371/journal.ppat.1011183.

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By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over the time course of infection was obtained. Data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows, especially in identifying the downregulated bacterial proteome response during infection progression by permitting quantification of low abundant bacterial proteins at early times of infection when bacterial infection load is low. S. Typhimurium invasion and replication specific proteomic signatures in epithelial cells revealed interdependent host/pathogen specific responses besides pointing to putative novel infection markers and signalling responses, including regulated host proteins associated with Salmonella-modified membranes.

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Jungblut, Peter R. "Proteome analysis of bacterial pathogens." Microbes and Infection 3, no. 10 (August 2001): 831–40. http://dx.doi.org/10.1016/s1286-4579(01)01441-1.

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Pappa, Eftychia, Heleni Vastardis, Manousos Makridakis, Jerome Zoidakis, Konstantinos Vougas, George Stamatakis, Martina Samiotaki, and Christos Rahiotis. "Analysis of Human and Microbial Salivary Proteomes in Children Offers Insights on the Molecular Pathogenesis of Molar-Incisor Hypomineralization." Biomedicines 10, no. 9 (August 24, 2022): 2061. http://dx.doi.org/10.3390/biomedicines10092061.

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Molar incisor hypomineralization is a complex developmental enamel defect that affects the permanent dentition of children with significant functional and aesthetic implications. Saliva is an ideal diagnostic tool and ensures patients’ compliance by diminishing the discomfort especially in pediatric population. Lately, salivary proteome analysis has progressively evolved in various biomedical disciplines. As changes in saliva composition are associated with oral diseases, it is reasonable to assume that the saliva proteome of MIH-affected children might be altered compared to healthy children. This study analyzed the human and microbial salivary proteome in children with MIH in order to identify salivary markers indicative of the pathology. The conducted proteomic analysis generated a comprehensive dataset comprising a total of 1515 high confidence identifications and revealed a clear discrimination between the two groups. Statistical comparison identified 142 differentially expressed proteins, while the pathway analysis indicated deregulation of inflammation, immune response mechanisms, and defense response to bacteria in MIH patients. Bacterial proteome analysis showed a lower diversity for the microbial species, which highlights the dysbiotic environment established in the MIH pathology.

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Marin, Lina Maria, Yizhi Xiao, Jaime Aparecido Cury, and Walter Luiz Siqueira. "Modulation of Streptococcus mutans Adherence to Hydroxyapatite by Engineered Salivary Peptides." Microorganisms 10, no. 2 (January 20, 2022): 223. http://dx.doi.org/10.3390/microorganisms10020223.

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Since the modification of the proteinaceous components of the Acquired Enamel Pellicle (AEP) could influence the adhesion of Streptococcus mutans, the most cariogenic bacteria, to dental surfaces, we assessed if engineered salivary peptides would affect the adherence and modulate the bacterial proteome upon adherence. Single-component AEPs were formed onto hydroxyapatite (HAp) discs by incubating them with statherin, histatin-3, DR9, DR9-DR9, DR9-RR14, RR14, and parotid saliva. Then, the discs were inoculated with S. mutans UA159 and the bacteria were allowed to adhere for 2 h, 4 h, and 8 h (n = 12/treatment/time point). The number of bacteria adhered to the HAp discs was determined at each time point and analyzed by two-way ANOVA and Bonferroni tests. Cell-wall proteins were extracted from adhered, planktonic, and inoculum (baseline) bacteria and proteome profiles were obtained after a bottom-up proteomics approach. The number of adhered bacteria significantly increased over time, being the mean values obtained at 8 h, from highest to lowest, as follows: DR9-RR14 > statherin > RR14 = DR9-DR9 > DR9 = histatin3 > saliva (p < 0.05). Treatments modulated the bacterial proteome upon adherence. The findings suggested a potential use of our engineered peptide DR9-DR9 to control S. mutans biofilm development by reducing bacterial colonization.

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Jabbour, Rabih E., Samir V. Deshpande, Mary Margaret Wade, Michael F. Stanford, Charles H. Wick, Alan W. Zulich, Evan W. Skowronski, and A. Peter Snyder. "Double-Blind Characterization of Non-Genome-Sequenced Bacteria by Mass Spectrometry-Based Proteomics." Applied and Environmental Microbiology 76, no. 11 (April 2, 2010): 3637–44. http://dx.doi.org/10.1128/aem.00055-10.

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ABSTRACT Due to the possibility of a biothreat attack on civilian or military installations, a need exists for technologies that can detect and accurately identify pathogens in a near-real-time approach. One technology potentially capable of meeting these needs is a high-throughput mass spectrometry (MS)-based proteomic approach. This approach utilizes the knowledge of amino acid sequences of peptides derived from the proteolysis of proteins as a basis for reliable bacterial identification. To evaluate this approach, the tryptic digest peptides generated from double-blind biological samples containing either a single bacterium or a mixture of bacteria were analyzed using liquid chromatography-tandem mass spectrometry. Bioinformatic tools that provide bacterial classification were used to evaluate the proteomic approach. Results showed that bacteria in all of the double-blind samples were accurately identified with no false-positive assignment. The MS proteomic approach showed strain-level discrimination for the various bacteria employed. The approach also characterized double-blind bacterial samples to the respective genus, species, and strain levels when the experimental organism was not in the database due to its genome not having been sequenced. One experimental sample did not have its genome sequenced, and the peptide experimental record was added to the virtual bacterial proteome database. A replicate analysis identified the sample to the peptide experimental record stored in the database. The MS proteomic approach proved capable of identifying and classifying organisms within a microbial mixture.

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Rohmer, Laurence, Tina Guina, Jinzhi Chen, Byron Gallis, Greg K. Taylor, Scott A. Shaffer, Samuel I. Miller, Mitchell J. Brittnacher, and David R. Goodlett. "Determination and Comparison of theFrancisella tularensissubsp.novicidaU112 Proteome to Other Bacterial Proteomes." Journal of Proteome Research 7, no. 5 (May 2, 2008): 2016–24. http://dx.doi.org/10.1021/pr700760z.

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Hoesl, Michael Georg, Stefan Oehm, Patrick Durkin, Elise Darmon, Lauri Peil, Hans-Rudolf Aerni, Juri Rappsilber, et al. "Chemical Evolution of a Bacterial Proteome." Angewandte Chemie International Edition 54, no. 34 (July 1, 2015): 10030–34. http://dx.doi.org/10.1002/anie.201502868.

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Bobadilla Fazzini, R. A., and Pilar Parada Valdecantos. "Analysis of Sulfur Metasecretome in Mixed Cultures of Acidithiobacillus Thiooxidans and Acidithiobacillus Ferrooxidans." Advanced Materials Research 71-73 (May 2009): 151–54. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.151.

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The role of biomolecules in bioleaching of copper sulphide minerals carried out by bacterial consortia with predominating acidithiobacilli species is of outmost interest. The proteomic analysis on bioleaching bacterial strains have been focused up to date on full Acidithiobacillus ferrooxidans proteome, allowing the identification of proteins belonging to the general stress response, phosphate limiting conditions and the ones linked to the periplasmic fraction. Our study shows for the first time the differential expression of secreted proteins by means of standard proteomics between pure cultures of Acidithiobacillus thiooxidans and in mixture with A. ferroxidans (metasecretome) grown in sulfur, where a set of proteins is de novo synthesized in the mixed culture, identifying an Omp40-like protein possibly related to bacterial adhesion, an hypothetical protein PSEEN2944 with unknown function and up-regulation of a cytochrome c biogenesis protein, findings that give an insight into the role of proteins at the sulfur – bacteria interface, highlighting the outputs of bacterial interactions in biomining environments at the protein secretion level.

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Quintela-Baluja, Marcos, Kelly Jobling, David W. Graham, Shamas Tabraiz, Burhan Shamurad, Mohamed Alnakip, Karola Böhme, Jorge Barros-Velázquez, Mónica Carrera, and Pilar Calo-Mata. "Rapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs." International Journal of Molecular Sciences 23, no. 22 (November 10, 2022): 13830. http://dx.doi.org/10.3390/ijms232213830.

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Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry.

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Navon, Sharon Penias, Guy Kornberg, Jin Chen, Tali Schwartzman, Albert Tsai, Elisabetta Viani Puglisi, Joseph D. Puglisi, and Noam Adir. "Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences." Proceedings of the National Academy of Sciences 113, no. 26 (June 15, 2016): 7166–70. http://dx.doi.org/10.1073/pnas.1606518113.

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Bioinformatic analysis of Escherichia coli proteomes revealed that all possible amino acid triplet sequences occur at their expected frequencies, with four exceptions. Two of the four underrepresented sequences (URSs) were shown to interfere with translation in vivo and in vitro. Enlarging the URS by a single amino acid resulted in increased translational inhibition. Single-molecule methods revealed stalling of translation at the entrance of the peptide exit tunnel of the ribosome, adjacent to ribosomal nucleotides A2062 and U2585. Interaction with these same ribosomal residues is involved in regulation of translation by longer, naturally occurring protein sequences. The E. coli exit tunnel has evidently evolved to minimize interaction with the exit tunnel and maximize the sequence diversity of the proteome, although allowing some interactions for regulatory purposes. Bioinformatic analysis of the human proteome revealed no underrepresented triplet sequences, possibly reflecting an absence of regulation by interaction with the exit tunnel.

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Schminke, Boris, Philipp Kauffmann, Phillipp Brockmeyer, Nicolai Miosge, Christof Lenz, and Andrea Schubert. "The Proteomes of Oral Cells Change during Co-Cultivation with Aggregatibacter actinomycetemcomitans and Eikenella corrodens." Biomedicines 11, no. 3 (February 24, 2023): 700. http://dx.doi.org/10.3390/biomedicines11030700.

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Background: Changes in the proteome of oral cells during periodontitis have rarely been investigated. This lack of information is partially attributed to the lack of human cell lines derived from the oral cavity for in vitro research. The objective of the present study was to create cell lines from relevant oral tissues and compare protein expression in cells cultured alone and in cells co-cultivated with periodontitis-associated bacterial strains. Methods: We established human cell lines of gingival keratinocytes, osteoblastic lineage cells from the alveolar bone, periodontal ligament fibroblasts, and cementum cells. Using state-of-the-art label-free mass spectrometry, we investigated changes in the proteomes of these cells after co-cultivation with Aggregatibacter actinomycetemcomitans and Eikenella corrodens for 48 h. Results: Gingival keratinocytes, representing ectodermal cells, exhibited decreased expression of specific keratins, basement membrane components, and cell-cell contact proteins after cultivation with the bacterial strains. Mesodermal lineage cells generally exhibited similar proteomes after co-cultivation with bacteria; in particular, collagens and integrins were expressed at higher levels. Conclusions: The results of the present study will help us elucidate the cellular mechanisms of periodontitis. Although co-cultivation with two periodontitis-associated bacterial strains significantly altered the proteomes of oral cells, future research is needed to examine the effects of complex biofilms mimicking in vivo conditions.

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Su, Jing, Bo Yao, Rong Huang, Xiaoni Liu, Zhenfen Zhang, and Yong Zhang. "Cross-Kingdom Pathogenesis of Pantoea alfalfae CQ10: Insights from Transcriptome and Proteome Analyses." Microorganisms 12, no. 11 (October 30, 2024): 2197. http://dx.doi.org/10.3390/microorganisms12112197.

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In grassland agroecosystems, some plant pathogenic bacteria can cause disease in animals. These strains are known as plant and animal cross-kingdom pathogenic bacteria. In this study, we established an alfalfa root infection model and a mouse model via the gavage administration of the Pantoea alfalfae CQ10 (CQ10) bacterial suspension. It was confirmed that the CQ10 strain caused bacterial leaf blight of alfalfa. Mice inoculated with 0.4 mL of 109 cfu/mL bacterial suspension developed clinical symptoms 48 h later, such as diminished vitality, tendencies to huddle, and lack of appetite, including severe lesions in stomach, liver, kidney, and spleen tissues. CQ10 strains were isolated from mouse feces at different time points of inoculation. Thus, CQ10 is a plant and animal cross-kingdom pathogenic bacterium. Transcriptome and proteome analyses showed that biofilm and iron uptake are important virulence factors of the pathogen CQ10, among which Bap and Lpp regulating biofilm are the key cross-kingdom virulence genes of CQ10. From an evolutionary perspective, insights gained from this dual animal–plant pathogen system may help to elucidate the molecular basis underlying the host specificity of bacterial pathogens. The result provides a theoretical basis for the risk assessment, prevention, and control strategies of new pathogenic bacteria entering a new region.

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Kurland, C. G., and S. G. E. Andersson. "Origin and Evolution of the Mitochondrial Proteome." Microbiology and Molecular Biology Reviews 64, no. 4 (December 1, 2000): 786–820. http://dx.doi.org/10.1128/mmbr.64.4.786-820.2000.

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SUMMARY The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral α-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from α-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the α-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific α-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.

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Kashirina, D. N., A. G. Brzhozovsky, S. V. Poddubko, А. А. Dymova, L. Kh Pastushkova, I. M. Larina, and O. I. Orlov. "EFFECT OF HYPOMAGNETIC ENVIRONMENT ON THE CELL PROTEOME OF BACTERIAL CULTURES." Aerospace and Environmental Medicine 59, no. 1 (2025): 34–43. https://doi.org/10.21687/0233-528x-2025-59-1-34-43.

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Investigations of differentially regulated molecular characteristics based on the results of panoramic profiling of bacterial cell lysate proteomes using chromatography-mass spectrometry and gene ontology analysis, identification of the enzymes involved in the metabolic activity and modification of the proteomes of strains cultivated in a hypomagnetic environment (HME) displayed dissimilar effects on lysate proteomes of epidermal staphylococci strains S1 and S3. Nonetheless, molecular responses of certain bacterial properties are alike. Both strains enlarged individual urease subunits (in S3, this was alpha-subunit only; in S1, these were alpha, beta and gamma subunits). Also, the strains increased levels of some pathogenicity factors, such as proteins associated with antibacterial resistance, DNAs, proteins binding to elastin and fibrinogen, and involved in biosynthesis of lipoteichoic acids essential for adhesion to epithelial cells. Although the number of samples was not large, these results demonstrate an obvious proteomic response to HME suggesting activation of the mechanisms which increase bacterial pathogenicity. This observation is of importance, specifically, for designing a habitable lunar base in near future.

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H. D. Sagawa, Cíntia, Renata de A. B. Assis, Paulo A. Zaini, Phillip A. Wilmarth, Brett S. Phinney, Leandro M. Moreira, and Abhaya M. Dandekar. "Proteome Analysis of Walnut Bacterial Blight Disease." International Journal of Molecular Sciences 21, no. 20 (October 9, 2020): 7453. http://dx.doi.org/10.3390/ijms21207453.

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The interaction between the plant host, walnut (Juglans regia; Jr), and a deadly pathogen (Xanthomonas arboricola pv. juglandis 417; Xaj) can lead to walnut bacterial blight (WB), which depletes walnut productivity by degrading the nut quality. Here, we dissect this pathosystem using tandem mass tag quantitative proteomics. Walnut hull tissues inoculated with Xaj were compared to mock-inoculated tissues, and 3972 proteins were identified, of which 3296 are from Jr and 676 from Xaj. Proteins with differential abundance include oxidoreductases, proteases, and enzymes involved in energy metabolism and amino acid interconversion pathways. Defense responses and plant hormone biosynthesis were also increased. Xaj proteins detected in infected tissues demonstrate its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Secreted proteases and extracellular secretion apparatus such as type IV pilus for twitching motility and type III secretion effectors indicate putative factors recognized by the host. Taken together, these results suggest intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Our results provide insights into molecular mechanisms and highlight potential molecular tools for early detection and disease control strategies.

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Vranakis, Iosif, Ioannis Goniotakis, Anna Psaroulaki, Vassilios Sandalakis, Yannis Tselentis, Kris Gevaert, and Georgios Tsiotis. "Proteome studies of bacterial antibiotic resistance mechanisms." Journal of Proteomics 97 (January 2014): 88–99. http://dx.doi.org/10.1016/j.jprot.2013.10.027.

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Guo, Monica S., and Carol A. Gross. "Stress-Induced Remodeling of the Bacterial Proteome." Current Biology 24, no. 10 (May 2014): R424—R434. http://dx.doi.org/10.1016/j.cub.2014.03.023.

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Poetsch, Ansgar, and María Inés Marchesini. "Proteomics of Brucella." Proteomes 8, no. 2 (April 22, 2020): 8. http://dx.doi.org/10.3390/proteomes8020008.

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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.

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Stubbs, Keith A., and David J. Vocadlo. "Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes." Australian Journal of Chemistry 62, no. 6 (2009): 521. http://dx.doi.org/10.1071/ch09140.

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As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.

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Möller, Jens, Fatemeh Nosratabadi, Luca Musella, Jörg Hofmann, and Andreas Burkovski. "Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum." Proteomes 9, no. 1 (March 13, 2021): 14. http://dx.doi.org/10.3390/proteomes9010014.

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Host-pathogen interactions are often studied in vitro using primary or immortal cell lines. This set-up avoids ethical problems of animal testing and has the additional advantage of lower costs. However, the influence of cell culture media on bacterial growth and metabolism is not considered or investigated in most cases. To address this question growth and proteome adaptation of Corynebacterium diphtheriae strain ISS3319 were investigated in this study. Bacteria were cultured in standard growth medium, cell culture medium, and fetal calf serum. Mass spectrometric analyses and label-free protein quantification hint at an increased bacterial pathogenicity when grown in cell culture medium as well as an influence of the growth medium on the cell envelope.

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Wongtrakoongate, Patompon, Sittiruk Roytrakul, Sukkid Yasothornsrikul, and Sumalee Tungpradabkul. "A Proteome Reference Map of the Causative Agent of MelioidosisBurkholderia pseudomallei." Journal of Biomedicine and Biotechnology 2011 (2011): 1–5. http://dx.doi.org/10.1155/2011/530926.

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Burkholderia pseudomalleiis the etiologic agent of melioidosis. Using 2DE and MALDI-TOF MS, we report here a proteome reference map constructed from early stationary phase, a bacterial adaptation process. We identified 282 protein spots representing 220 ORFs; many of them have been implicated in bacterial pathogenesis. Up to 20% of identified ORFs belong to post-translational modification and stress responses. The proteome reference map will support future analysis of the bacterial gene and environmental regulation and facilitate comparative proteomics with its sibling species.

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Noh, Susan M., Kelly A. Brayton, Wendy C. Brown, Junzo Norimine, Gerhard R. Munske, Christine M. Davitt, and Guy H. Palmer. "Composition of the Surface Proteome of Anaplasma marginale and Its Role in Protective Immunity Induced by Outer Membrane Immunization." Infection and Immunity 76, no. 5 (March 3, 2008): 2219–26. http://dx.doi.org/10.1128/iai.00008-08.

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ABSTRACT Surface proteins of tick-borne, intracellular bacterial pathogens mediate functions essential for invasion and colonization. Consequently, the surface proteome of these organisms is specifically relevant from two biological perspectives, induction of protective immunity in the mammalian host and understanding the transition from the mammalian host to the tick vector. In this study, the surface proteome of Anaplasma marginale, a tick-transmitted bacterial pathogen, was targeted by using surface-specific cross-linking to form intermolecular bonds between adjacent proteins. Liquid chromatography and tandem mass spectroscopy were then employed to characterize the specific protein composition of the resulting complexes. The surface complexes of A. marginale isolated from erythrocytes of the mammalian host were composed of multiple membrane proteins, most of which belong to a protein family, pfam01617, which is conserved among bacteria in the genus Anaplasma and the closely related genus Ehrlichia. In contrast, the surface proteome of A. marginale isolated from tick cells was much less complex and contained a novel protein, AM778, not identified within the surface proteome of organisms from the mammalian host. Immunization using the cross-linked surface complex induced protection against high-level bacteremia and anemia upon A. marginale challenge of cattle and effectively recapitulated the protection induced by immunization with whole outer membranes. These results indicate that a surface protein subset of the outer membrane is capable of inducing protective immunity and serves to direct vaccine development. Furthermore, the data support that remodeling of the surface proteome accompanies the transition between mammalian and arthropod hosts and identify novel targets for blocking transmission.

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Tsuchida, Sachio, and Tomohiro Nakayama. "MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification." Applied Sciences 12, no. 6 (March 9, 2022): 2814. http://dx.doi.org/10.3390/app12062814.

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The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.

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Scott, Nichollas E., and Elizabeth L. Hartland. "The role of mass spectrometry analysis in bacterial effector characterization." Biochemical Journal 474, no. 16 (August 7, 2017): 2779–84. http://dx.doi.org/10.1042/bcj20160797.

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Many secreted bacterial effector proteins play a critical role in host–pathogen interactions by mediating a variety of post-translational modifications, some of which do not occur natively within the eukaryotic proteome. The characterization of bacterial effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS) and proteomic approaches are also playing an indispensable role. The focus of this editorial is to highlight the strengths of specific MS approaches and their utility for the characterization of bacterial effector activity. With the capability of new generation MS instrumentation, MS-based technologies can provide information that is inaccessible using traditional molecular or immunochemical approaches.

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Dori-Bachash, Mally, Bareket Dassa, Shmuel Pietrokovski, and Edouard Jurkevitch. "Proteome-Based Comparative Analyses of Growth Stages Reveal New Cell Cycle-Dependent Functions in the Predatory Bacterium Bdellovibrio bacteriovorus." Applied and Environmental Microbiology 74, no. 23 (October 3, 2008): 7152–62. http://dx.doi.org/10.1128/aem.01736-08.

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ABSTRACT Bdellovibrio and like organisms are obligate predators of bacteria that are ubiquitously found in the environment. Most exhibit a peculiar dimorphic life cycle during which free-swimming attack-phase (AP) cells search for and invade bacterial prey cells. The invader develops in the prey as a filamentous polynucleoid-containing cell that finally splits into progeny cells. Therapeutic and biocontrol applications of Bdellovibrio in human and animal health and plant health, respectively, have been proposed, but more knowledge of this peculiar cell cycle is needed to develop such applications. A proteomic approach was applied to study cell cycle-dependent expression of the Bdellovibrio bacteriovorus proteome in synchronous cultures of a facultative host-independent (HI) strain able to grow in the absence of prey. Results from two-dimensional gel electrophoresis, mass spectrometry, and temporal expression of selected genes in predicted operons were analyzed. In total, about 21% of the in silico predicted proteome was covered. One hundred ninety-six proteins were identified, including 63 hitherto unknown proteins and 140 life stage-dependent spots. Of those, 47 were differentially expressed, including chemotaxis, attachment, growth- and replication-related, cell wall, and regulatory proteins. Novel cell cycle-dependent adhesion, gliding, mechanosensing, signaling, and hydrolytic functions were assigned. The HI model was further studied by comparing HI and wild-type AP cells, revealing that proteins involved in DNA replication and signaling were deregulated in the former. A complementary analysis of the secreted proteome identified 59 polypeptides, including cell contact proteins and hydrolytic enzymes specific to predatory bacteria.

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Qiu, Huan, Dana C. Price, Andreas P. M. Weber, Fabio Facchinelli, Hwan Su Yoon, and Debashish Bhattacharya. "Assessing the bacterial contribution to the plastid proteome." Trends in Plant Science 18, no. 12 (December 2013): 680–87. http://dx.doi.org/10.1016/j.tplants.2013.09.007.

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van Olst, Berdien, Avis Nugroho, Sjef Boeren, Jacques Vervoort, Herwig Bachmann, and Michiel Kleerebezem. "Bacterial proteome adaptation during fermentation in dairy environments." Food Microbiology 121 (August 2024): 104514. http://dx.doi.org/10.1016/j.fm.2024.104514.

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Huang, Chuan, Hoa-Quynh Pham, Lina Zhu, Rui Wang, Oi-Kwan Law, Shu-Ling Lin, Qi-Chang Nie, Liang Zhang, Xin Wang, and Terrence Chi-Kong Lau. "Comparative Analysis of Transcriptome and Proteome Revealed the Common Metabolic Pathways Induced by Prevalent ESBL Plasmids in Escherichia coli." International Journal of Molecular Sciences 24, no. 18 (September 12, 2023): 14009. http://dx.doi.org/10.3390/ijms241814009.

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Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often neglecting the complete functional role of multidrug-resistant (MDR) plasmids in bacteria. In this study, we conducted a comprehensive investigation of the transcriptomes and proteomes of Escherichia coli J53 transconjugants harboring six major MDR plasmids of different incompatibility (Inc) groups, which were clinically isolated from patients. The RNA-seq analysis revealed that MDR plasmids influenced the gene expression in the bacterial host, in particular, the genes related to metabolic pathways. A proteomic analysis demonstrated the plasmid-induced regulation of several metabolic pathways including anaerobic respiration and the utilization of various carbon sources such as serine, threonine, sialic acid, and galactarate. These findings suggested that MDR plasmids confer a growth advantage to bacterial hosts in the gut, leading to the expansion of plasmid-carrying bacteria over competitors without plasmids. Moreover, this study provided insights into the versatility of prevalent MDR plasmids in moderating the cellular gene network of bacteria, which could potentially be utilized in therapeutics development for bacteria carrying MDR plasmids.

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Thompson, Catriona M. A., James P. J. Hall, Govind Chandra, Carlo Martins, Gerhard Saalbach, Supakan Panturat, Susannah M. Bird, et al. "Plasmids manipulate bacterial behaviour through translational regulatory crosstalk." PLOS Biology 21, no. 2 (February 14, 2023): e3001988. http://dx.doi.org/10.1371/journal.pbio.3001988.

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Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host’s translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.

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Stensballe, Allan, Jacob Skallerup Andersen, Christopher Aboo, Anders Borg Andersen, Jie Ren, Michael Kruse Meyer, Kate Lykke Lambertsen, and Peter Derek Christian Leutscher. "Naïve Inflammatory Proteome Profiles of Glucocorticoid Responsive Polymyalgia Rheumatica and Rheumatic Arthritis Patients—Links to Triggers and Proteomic Manifestations." Journal of Personalized Medicine 14, no. 5 (April 25, 2024): 449. http://dx.doi.org/10.3390/jpm14050449.

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Polymyalgia rheumatica (PMR) is an inflammatory disorder of unknown etiology, sharing symptoms with giant cell arthritis (GCA) and rheumatoid arthritis (RA). The pathogenic inflammatory roots are still not well understood, and there is a lack of extensive biomarker studies to explain the disease debut and post-acute phase. This study aimed to deeply analyze the serum proteome and inflammatory response of PMR patients before and after glucocorticoid treatment. We included treatment-naïve PMR patients, collecting samples before and after 3 months of treatment. For comparison, disease-modifying antirheumatic drug (DMARD)-naïve RA patients were included and matched to healthy controls (CTL). The serum proteome was examined using label-free quantitative mass spectrometry, while inflammation levels were assessed using multiplex inflammatory cytokine and cell-free DNA assays. The serum proteomes of the four groups comprised acute phase reactants, coagulation factors, complement proteins, immunoglobulins, and apolipoproteins. Serum amyloid A (SAA1) was significantly reduced by active PMR treatment. Cell-free DNA levels in PMR and RA groups were significantly higher than in healthy controls due to acute inflammation. Complement factors had minimal changes post-treatment. The individual serum proteome in PMR patients showed over 100 abundantly variable proteins, emphasizing the systemic impact of PMR disease debut and the effect of treatment. Interleukin (IL)-6 and interferon-gamma (IFN-γ) were significantly impacted by glucocorticoid treatment. Our study defines the PMR serum proteome during glucocorticoid treatment and highlights the role of SAA1, IL-6, and IFN-γ in treatment responses. An involvement of PGLYRP2 in acute PMR could indicate a response to bacterial infection, highlighting its role in the acute phase of the immune response. The results suggest that PMR may be an aberrant response to a bacterial infection with an exacerbated IL-6 and acute phase inflammatory response and molecular attempts to limit the inflammation.

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Karanja, Caroline W., Nimishetti Naganna, Nader S. Abutaleb, Neetu Dayal, Kenneth I. Onyedibe, Uma Aryal, Mohamed N. Seleem, and Herman O. Sintim. "Isoquinoline Antimicrobial Agent: Activity against Intracellular Bacteria and Effect on Global Bacterial Proteome." Molecules 27, no. 16 (August 10, 2022): 5085. http://dx.doi.org/10.3390/molecules27165085.

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A new class of alkynyl isoquinoline antibacterial compounds, synthesized via Sonogashira coupling, with strong bactericidal activity against a plethora of Gram-positive bacteria including methicillin- and vancomycin-resistant Staphylococcus aureus (S. aureus) strains is presented. HSN584 and HSN739, representative compounds in this class, reduce methicillin-resistant S. aureus (MRSA) load in macrophages, whilst vancomycin, a drug of choice for MRSA infections, was unable to clear intracellular MRSA. Additionally, both HSN584 and HSN739 exhibited a low propensity to develop resistance. We utilized comparative global proteomics and macromolecule biosynthesis assays to gain insight into the alkynyl isoquinoline mechanism of action. Our preliminary data show that HSN584 perturb S. aureus cell wall and nucleic acid biosynthesis. The alkynyl isoquinoline moiety is a new scaffold for the development of potent antibacterial agents against fatal multidrug-resistant Gram-positive bacteria.

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Volkov, Mikhail, Arieke S. B. Kampstra, Karin A. J. van Schie, Anouk G. van Mourik, Joanneke C. Kwekkeboom, Arnoud de Ru, Peter A. van Veelen, Tom W. J. Huizinga, René E. M. Toes, and Diane van der Woude. "Acetylated bacterial proteins as potent antigens inducing an anti-modified protein antibody response." RMD Open 10, no. 3 (July 2024): e004411. http://dx.doi.org/10.1136/rmdopen-2024-004411.

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ObjectiveGut-residing bacteria, such asEscherichia coli, can acetylate their proteome under conditions of amine starvation. It is postulated that the (gut) microbiome is involved in the breach of immune tolerance to modified self-proteins leading to the anti-modified protein antibodies (AMPAs), hallmarking seropositive rheumatoid arthritis (RA). Our aim was to determine whether acetylated bacterial proteins can induce AMPA responses cross-reactive to modified self-proteins and be recognised by human AMPA (hAMPA).MethodsE. colibacteria were grown under amine starvation to generate endogenously acetylated bacterial proteins. Furthermore,E. coliproteins were acetylated chemically. Recognition of these proteins by hAMPA was analysed by western blotting and ELISA; recognition by B cells carrying a modified protein-reactive B cell receptor (BCR) was analysed by pSyk (Syk phosphorylation) activation assay. C57BL/6 mice were immunised with (modified) bacterial protein fractions, and sera were analysed by ELISA.ResultsChemically modified bacterial protein fractions contained high levels of acetylated proteins and were readily recognised by hAMPA and able to activate B cells carrying modified protein-reactive BCRs. Likely due to substantially lower levels of acetylation, endogenously acetylated protein fractions were not recognised by hAMPA or hAMPA-expressing B cells. Immunising mice with chemically modified protein fractions induced a strong cross-reactive AMPA response, targeting various modified antigens including citrullinated proteins.ConclusionsAcetylated bacterial proteins are recognisable by hAMPA and are capable of inducing cross-reactive AMPA in mice. These observations provide the first conceptual evidence for a novel mechanism involving the (endogenous) acetylation of the bacterial proteome, allowing a breach of tolerance to modified proteins and the formation of cross-reactive AMPA.

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Tsakou, Foteini, Rosa Jersie-Christensen, Håvard Jenssen, and Biljana Mojsoska. "The Role of Proteomics in Bacterial Response to Antibiotics." Pharmaceuticals 13, no. 9 (August 27, 2020): 214. http://dx.doi.org/10.3390/ph13090214.

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For many years, we have tried to use antibiotics to eliminate the persistence of pathogenic bacteria. However, these infectious agents can recover from antibiotic challenges through various mechanisms, including drug resistance and antibiotic tolerance, and continue to pose a global threat to human health. To design more efficient treatments against bacterial infections, detailed knowledge about the bacterial response to the commonly used antibiotics is required. Proteomics is a well-suited and powerful tool to study molecular response to antimicrobial compounds. Bacterial response profiling from system-level investigations could increase our understanding of bacterial adaptation, the mechanisms behind antibiotic resistance and tolerance development. In this review, we aim to provide an overview of bacterial response to the most common antibiotics with a focus on the identification of dynamic proteome responses, and through published studies, to elucidate the formation mechanism of resistant and tolerant bacterial phenotypes.

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Lim, Sooa. "A Review of the Bacterial Phosphoproteomes of Beneficial Microbes." Microorganisms 11, no. 4 (April 3, 2023): 931. http://dx.doi.org/10.3390/microorganisms11040931.

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The number and variety of protein post-translational modifications (PTMs) found and characterized in bacteria over the past ten years have increased dramatically. Compared to eukaryotic proteins, most post-translational protein changes in bacteria affect relatively few proteins because the majority of modified proteins exhibit substoichiometric modification levels, which makes structural and functional analyses challenging. In addition, the number of modified enzymes in bacterial species differs widely, and degrees of proteome modification depend on environmental conditions. Nevertheless, evidence suggests that protein PTMs play essential roles in various cellular processes, including nitrogen metabolism, protein synthesis and turnover, the cell cycle, dormancy, spore germination, sporulation, persistence, and virulence. Additional investigations on protein post-translational changes will undoubtedly close knowledge gaps in bacterial physiology and create new means of treating infectious diseases. Here, we describe the role of the post-translation phosphorylation of major bacterial proteins and review the progress of research on phosphorylated proteins depending on bacterial species.

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Schwartz, Russell, Claire S. Ting, and Jonathan King. "Whole Proteome pI Values Correlate with Subcellular Localizations of Proteins for Organisms within the Three Domains of Life." Genome Research 11, no. 5 (April 11, 2001): 703–9. http://dx.doi.org/10.1101/gr.158701.

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Isoelectric point (pI) values have long been a standard measure for distinguishing between proteins. This article analyzes distributions of pI values estimated computationally for all predicted ORFs in a selection of fully sequenced genomes. Histograms of pI values confirm the bimodality that has been observed previously for bacterial and archaeal genomes (Van Bogelen et al. 1999) and reveal a trimodality in eukaryotic genomes. A similar analysis on subsets of a nonredundant protein sequence database generated from the full database by selecting on subcellular localization shows that sequences annotated as corresponding to cytosolic and integral membrane proteins have pI distributions that appear to correspond with the two observed modes of bacteria and archaea. Furthermore, nuclear proteins have a broader distribution that may account for the third mode observed in eukaryotes. On the basis of this association between pI and subcellular localization, we conclude that the bimodal character of whole proteome pI values in bacteria and archaea and the trimodal character in eukaryotes are likely to be general properties of proteomes and are associated with the need for different pI values depending on subcellular localization. Our analyses also suggest that the proportions of proteomes consisting of membrane-associated proteins may be currently underestimated.

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Schoberleitner, Ines, Leoni Baier, Michaela Lackner, Lisa-Maria Zenz, Débora C. Coraça-Huber, Wendy Ullmer, Annabelle Damerum, et al. "Surface Topography, Microbial Adhesion, and Immune Responses in Silicone Mammary Implant-Associated Capsular Fibrosis." International Journal of Molecular Sciences 25, no. 6 (March 9, 2024): 3163. http://dx.doi.org/10.3390/ijms25063163.

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Breast cancer is the most common cancer in women globally, often necessitating mastectomy and subsequent breast reconstruction. Silicone mammary implants (SMIs) play a pivotal role in breast reconstruction, yet their interaction with the host immune system and microbiome remains poorly understood. This study investigates the impact of SMI surface topography on host antimicrobial responses, wound proteome dynamics, and microbial colonization. Biological samples were collected from ten human patients undergoing breast reconstruction with SMIs. Mass spectrometry profiles were analyzed for acute and chronic wound proteomes, revealing a nuanced interplay between topography and antimicrobial response proteins. 16S rRNA sequencing assessed microbiome dynamics, unveiling topography-specific variations in microbial composition. Surface topography alterations influenced wound proteome composition. Microbiome analysis revealed heightened diversity around rougher SMIs, emphasizing topography-dependent microbial invasion. In vitro experiments confirmed staphylococcal adhesion, growth, and biofilm formation on SMI surfaces, with increased texture correlating positively with bacterial colonization. This comprehensive investigation highlights the intricate interplay between SMI topography, wound proteome dynamics, and microbial transmission. The findings contribute to understanding host–microbe interactions on SMI surfaces, essential for optimizing clinical applications and minimizing complications in breast reconstruction.

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Erdmann, Jelena, Janne G. Thöming, Sarah Pohl, Andreas Pich, Christof Lenz, and Susanne Häussler. "The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates." Cells 8, no. 10 (September 23, 2019): 1129. http://dx.doi.org/10.3390/cells8101129.

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Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.

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Subramaniam, Nirojah, Jenny Bottek, Stephanie Thiebes, Kristina Zec, Matthias Kudla, Camille Soun, Elena de Dios Panal, et al. "Proteomic and bioinformatic profiling of neutrophils in CLL reveals functional defects that predispose to bacterial infections." Blood Advances 5, no. 5 (March 2, 2021): 1259–72. http://dx.doi.org/10.1182/bloodadvances.2020002949.

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Abstract Patients with chronic lymphocytic leukemia (CLL) typically suffer from frequent and severe bacterial infections. Although it is well known that neutrophils are critical innate immune cells facilitating the early defense, the underlying phenotypical and functional changes in neutrophils during CLL remain largely elusive. Using a murine adoptive transfer model of CLL, we demonstrate aggravated bacterial burden in CLL-bearing mice upon a urinary tract infection with uropathogenic Escherichia coli. Bioinformatic analyses of the neutrophil proteome revealed increased expression of proteins associated with interferon signaling and decreased protein expression associated with granule composition and neutrophil migration. Functional experiments validated these findings by showing reduced levels of myeloperoxidase and acidification of neutrophil granules after ex vivo phagocytosis of bacteria. Pathway enrichment analysis indicated decreased expression of molecules critical for neutrophil recruitment, and migration of neutrophils into the infected urinary bladder was significantly reduced. These altered migratory properties of neutrophils were also associated with reduced expression of CD62L and CXCR4 and correlated with an increased incidence of infections in patients with CLL. In conclusion, this study describes a molecular signature of neutrophils through proteomic, bioinformatic, and functional analyses that are linked to a reduced migratory ability, potentially leading to increased bacterial infections in patients with CLL.

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Karlberg, Olof, Björn Canbäck, Charles G. Kurland, and Siv G. E. Andersson. "The Dual Origin of the Yeast Mitochondrial Proteome." Yeast 1, no. 3 (January 1, 2000): 170–87. http://dx.doi.org/10.1155/2000/597406.

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We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.

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Karlberg, Olof, Björn Canbäck, Charles G. Kurland, and Siv G. E. Andersson. "The Dual Origin of the Yeast Mitochondrial Proteome." Yeast 1, no. 3 (2000): 170–87. http://dx.doi.org/10.1002/1097-0061(20000930)17:3<170::aid-yea25>3.0.co;2-v.

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Анотація:

We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.

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Goemans, Camille V., and Jean-François Collet. "Stress-induced chaperones: a first line of defense against the powerful oxidant hypochlorous acid." F1000Research 8 (September 23, 2019): 1678. http://dx.doi.org/10.12688/f1000research.19517.1.

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Hypochlorous acid (HOCl; bleach) is a powerful weapon used by our immune system to eliminate invading bacteria. Yet the way HOCl actually kills bacteria and how they defend themselves from its oxidative action have only started to be uncovered. As this molecule induces both protein oxidation and aggregation, bacteria need concerted efforts of chaperones and antioxidants to maintain proteostasis during stress. Recent advances in the field identified several stress-activated chaperones, like Hsp33, RidA, and CnoX, which display unique structural features and play a central role in protecting the bacterial proteome during HOCl stress.

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Tyuri, Yu A., A. Z. Zaripova, G. Sh Isaeva, I. G. Mustafin, and L. T. Bayazitova. "Proteomic technologies in the development of new vaccines based on serotype-non-specific protein antigens of Streptococcus pneumoniae." Kazan medical journal 100, no. 4 (July 31, 2019): 680–88. http://dx.doi.org/10.17816/kmj2019-680.

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The review presents a modern strategy to improve the means of vaccine prevention of streptococcal infections aimed at finding and developing new vaccines for immunization of people belonging to risk groups. It should be noted that pneumococci (S. pneumoniae) are members of gram-positive bacteria (diplococci) and become the main cause of various nosological forms of human infectious diseases (such as pneumonia, otitis media, sinusitis, bacteremia and meningitis). Existing pneumococcal vaccines (conjugate and polysaccharide) have some important limitations, for example, serotype dependence, loss of effectiveness due to a change in the serotype landscape, insufficient protective effect from non-invasive forms of pneumococcal infections and high production costs associated with the development of these products. The main part of the review presents the most important research papers that used modern proteomic technologies in the study of the S. pneumoniae proteomic profile. These works allow us to evaluate at the molecular level the importance of bacterial proteins as candidates for creating new combination vaccines that can effectively protect against the full range of pneumococcal serotypes circulating in the human population. So, in particular, the data are provided on the new methodology for the analysis of the proteome of extracellular S. pneumoniae bacterial microvesicles to identify immunoreactive protein antigens, potential candidates for inclusion into vaccines. As a result of these studies, 15 immunoreactive proteins were discovered, 7 of which are cytosolic and 8 proteins are bound to the cell surface (MalX, ABC transporter or substrate binding transport protein, AmiA, AliA, LytC, IgA1 protease, PspA and the putative precursor of β-galactosidase). These are possible candidates for developing combination vaccines. Additionally, the review presents data on the role of significant virulence factors of the protein nature of S. pneumoniae strains in nasopharyngeal colonization, increased infectivity, as well as on overcoming reactions of the host's immune response.

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Trost, Brett, Anthony Kusalik, Guglielmo Lucchese, and Darja Kanduc. "Bacterial peptides are intensively present throughout the human proteome." Self/Nonself 1, no. 1 (January 2010): 71–74. http://dx.doi.org/10.4161/self.1.1.9588.

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Danielsen, Marianne, Henrik Hornshøj, Richard H. Siggers, Bent Borg Jensen, Andrew G. van Kessel, and Emøke Bendixen. "Effects of Bacterial Colonization on the Porcine Intestinal Proteome." Journal of Proteome Research 6, no. 7 (July 2007): 2596–604. http://dx.doi.org/10.1021/pr070038b.

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Meydan, Sezen, James Marks, Dorota Klepacki, Virag Sharma, Pavel V. Baranov, Andrew E. Firth, Tōnu Margus, Amira Kefi, Nora Vázquez-Laslop, and Alexander S. Mankin. "Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome." Molecular Cell 74, no. 3 (May 2019): 481–93. http://dx.doi.org/10.1016/j.molcel.2019.02.017.

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Han, Junlong, Shuhong Yi, Xinlu Zhao, Yundan Zheng, Donghong Yang, Gaofei Du, Xiao-Yan Yang, Qing-Yu He, and Xuesong Sun. "Improved SILAC method for double labeling of bacterial proteome." Journal of Proteomics 194 (March 2019): 89–98. http://dx.doi.org/10.1016/j.jprot.2018.12.011.

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