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Results for “proteome mapping”

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PubMed2026

Proteomic insights into Helicobacter pylori infection in stomach cells, revealing host response and host-targeted therapeutics repurposing.

BACKGROUND: Helicobacter pylori (H. pylori) is a globally prevalent gastric pathogen strongly associated with chronic gastritis, peptic ulcers, and gastric cancer. While bacterial factors have been extensively studied, host proteomic responses and their therapeutic potential remain largely underexplored. RESEARCH DESIGN AND METHODS: Current analyses employed a systematic proteomics-based data integration and harmonization approach (retrospective qualitative cohort study) to identify important differentially regulated host proteins. Proteomic datasets were curated from in vitro studies and analyzed for functional enrichment, protein-protein interaction networks, and hub protein identification. To explore therapeutic repurposing, drug repositioning was performed using the DrugBank database. RESULTS: Data summation describing protein differential regulation in human gastric cells as a result of the infection revealed 1672 perturbed host proteins. Bioinformatics analysis revealed 11 proteins including CSK, MET, RELA, MARK2, GRB2, FTO, PLCG1, CRKL, RPS5, RPS9, and RPS27A to be ideal host targets for therapeutic repurposing. Clinically approved drugs such as Dasatinib (targeting CSK) and Crizotinib (targeting MET) emerged as promising candidates due to favorable pharmacokinetics and known bioactivity. CONCLUSIONS: Host-directed therapeutics could offer alternative strategies to conventional antibiotic therapy, addressing challenges such as resistance and infection recurrence, providing a foundation for future experimental validation and development of host-targeted interventions for infection control.

Humans↗
PubMed2004

Grape berry biochemistry revisited upon proteomic analysis of the mesocarp.

Major soluble proteins of grapevine ripe berries were extracted from six different cultivars including non vinifera, with trichloroacetic acid acetone and resolved in two-dimensional electrophoresis (2-DE) gels. About three hundred spots were detected on the 2-DE map after colloidal blue staining. From 2-DE map of cv. Gamay mesocarp, 67 proteins were identified (p > 0.95) using matrix-assisted laser desorption/ionization-mass spectrometry analysis. About 34%, 19%, and 13% of identified proteins play, respectively, a role in energy metabolism, defense, and stress response and primary metabolism. 2-DE analysis revealed considerable accumulation of dehydrin, invertase, and a putative transcription factor in the ripe fruit, in addition to pathogenesis-related proteins such as chitinase and thaumatin-like proteins previously documented as prevalent proteins in ripe berries. Actual translation of redundant transcripts of unclear function such as Grip31, Grip32, and Grip61 recently cloned in ripe grape berries was confirmed. The relative abundance of UDP-glucose pyrophosphorylase and vacuolar invertase strongly supported a key role of the apoplastic pathway of sugar loading during ripening. Comparative analysis shows that differences between cultivars were low, but different isoforms of alcohol dehydrogenase and of a transcription factor of hexose transporter were obvious in the six cultivars. Peptide mass fingerprinting suggests that the Adh isoforms would be Adh2/Adh6 or Adh2/Adh7 dimers and unambiguously shows that considerable deletion/insertion inside Adh7 are not cloning artifacts.

Electrophoresis, Gel, Two-Dimensional↗
PubMedDate not supplied

Interaction proteomics.

The term proteome is traditionally associated with the identification of a large number of proteins within complex mixtures originating from a given organelle, cell or even organism. Current proteome investigations are basically focused on two major areas, expression proteomics and functional proteomics. Both approaches rely on the fractionation of protein mixtures essentially by two-dimensional polyacrylamide gel electrophoresis (2D-gel) and the identification of individual protein bands by mass spectrometric techniques (2D-MS). Functional proteomics approaches are basically addressing two main targets, the elucidation of the biological function of unknown proteins and the definition of cellular mechanisms at the molecular level. In the cell many processes are governed not only by the relative abundance of proteins but also by rapid and transient regulation of activity, association and localization of proteins and protein complexes. The association of an unknown protein with partners belonging to a specific protein complex involved in a particular process would then be strongly suggestive of its biological function. The identification of interacting proteins in stable complexes in a cellular system is essentially achieved by affinity-based procedures. Different strategies relying on this simple concept have been developed and a brief overview of the main approaches presently used in functional proteomics studies is described.

Chromatography, Affinity↗
PubMed2004

Protein interaction networks in bacteria.

The complement of expressed cellular proteins - the proteome - is organized into functional, structured networks of protein interactions that mediate assembly of molecular machines and dynamic cellular pathways. Recent studies reveal the biological roles of protein interactions in bacteriophage T7 and Helicobacter pylori, and new methods allow to compare and to predict interaction networks in other species. Smaller scale networks provide biological insights into DNA replication and chromosome dynamics in Bacillus subtilis and Archeoglobus fulgidus, and into the assembly of multiprotein complexes such as the type IV secretion system of Agrobacterium tumefaciens, and the cell division machinery of Escherichia coli. Genome-wide interaction networks in several species are needed to obtain a biologically meaningful view of the higher order organization of the proteome in bacteria.

Bacteria↗
PubMed2001

Proteomics--post-genomic cartography to understand gene function.

The completion of the genomic sequences of numerous organisms from human and mouse to Caenorhabditis elegans and many microorganisms, and the definition of their genes provides a database to interpret cellular protein-expression patterns and relate them to protein function. Proteomics technologies that are dependent on mass spectrometry and involve two-dimensional gel electrophoresis are providing the main window into the world of differential protein-expression analysis. In this article, the limitations and expectations of this research field are examined and the future of the analytical needs of proteomics is explored.

Animals↗
PubMed2002

Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective.

We employed a combination of tandem affinity purification and mass spectrometry for deciphering protein complexes and the protein interaction network in budding yeast. 53 genes were epitope-tagged, and their interaction partners were isolated by two-step immunoaffinity chromatography from whole cell lysates. 38 baits pulled down a total of 220 interaction partners, which are members of 19 functionally distinct protein complexes. We identified four proteins shared between complexes of different functionality thus charting segments of a protein interaction network. Concordance with the results of genome-wide two-hybrid screening was poor (14% of identified interactors overlapped) suggesting that the two approaches may provide complementary views on physical interactions within the proteome.

Chromatography, Affinity↗
PubMed2004

Impact of 'ome' analyses on inverse metabolic engineering.

Genome-wide or large-scale methodologies employed in functional genomics such as DNA sequencing, transcription profiling, proteomics, and metabolite profiling have become important tools in many metabolic engineering strategies. These techniques allow the identification of genetic differences and insight into their cellular effects. In the field of inverse metabolic engineering mapping of differences between strains with different degree of a certain desired phenotype and subsequent identification of factors conferring that phenotype are an essential part. Therefore, the tools of functional genomics in particular have the potential to promote and expand inverse metabolic engineering. Here, we review the use of functional genomics methods in inverse metabolic engineering, examples are presented, and we discuss the identification of targets for metabolic engineering with low fold changes using these techniques.

Animals↗
PubMed2006

Proteomic analysis of pathogenic bacterium Vibrio vulnificus.

In this study we have constructed a proteome reference map of the pathogenic bacterium Vibrio vulnificus. From the reference map, we identified several virulence-related proteins, such as ToxR and ToxS, as well as numerous proteins involved in diverse cellular functions. To search for additional virulence-related proteins, we compared the whole proteomes from the wild-type and toxR mutant of V. vulnificus and found that several proteins were up- or down-regulated in the toxR mutant. We suggest that these differentially regulated proteins whose expression is coordinately controlled by a virulence regulator ToxR, some of which are already implicated in virulence, play roles in the pathogenesis of V. vulnificus.

Bacterial Proteins↗
PubMed2000

Proteomic databases and software on the web.

In the wake of sequencing projects, protein function analysis is evolving fast, from the careful design of assays that address specific questions to 'large-scale' proteomics technologies that yield proteome-wide maps of protein expression or interaction. As these new technologies depend heavily on information storage, representation and analysis, existing databases and software tools are being adapted, while new resources are emerging. This paper describes the proteomics databases and software available through the World-Wide Web, focusing on their present use and applicability. As the resource situation is highly transitory, trends and probable evolutions are discussed whenever applicable.

Computational Biology↗
PubMed2006

Organellar proteomics: turning inventories into insights.

Subcellular organization is yielding to large-scale analysis. Researchers are now applying robust mass-spectrometry-based proteomics methods to obtain an inventory of biochemically isolated organelles that contain hundreds of proteins. High-resolution methods allow accurate protein identification, and novel algorithms can distinguish genuine from co-purifying components. Organellar proteomes have been analysed by bioinformatic methods and integrated with other large-scale data sets. The dynamics of organelles can also be studied by quantitative proteomics, which offers powerful methods that are complementary to fluorescence-based microscopy. Here, we review the emerging trends in this rapidly expanding area and discuss the role of organellar proteomics in the context of functional genomics and systems biology.

Animals↗
PubMed2004

Proteome characterization of human T helper 1 and 2 cells.

T helper (Th) cells can be polarized into two different main subtypes, Th1 and Th2 cells. Their activation is linked to the eradication of different pathogens and to dissimilar immunological dysfunctions, which implies differences also in their protein expression patterns. To identify these differences, CD4(+) T cells were isolated from human cord blood, polarized in vitro to Th1 and Th2 and activated via CD3 and CD28. Cells were lysed, soluble proteins were separated with two-dimensional electrophoresis and differing protein spots were identified with peptide mass fingerprinting. The expression of 14 proteins differed in Th1 and Th2 cells after both 7 and 14 days of polarization. Twelve of the proteins could be identified, most of which are new in this context. Two proteins were differentially modified in the two cell types. Especially, N-terminal acetylation of cyclophilin A was stronger in Th1 than in Th2 cells. To compare the RNA and the protein levels of the identified genes, mRNA expression was measured with Affymetrix oligonucleotide microarrays (HG-U133A). The mRNA and protein expression level correlated only in six cases out of eleven, which highlights the complementary roles that proteomics and transcriptomics have in the elucidation of biological phenomena.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2002

Proteomics and the kidney.

Proteomics can be defined as "the systematic analysis of proteins for their identity, quantity, and function." The central concept is "multiplexing," i.e., simultaneous analysis of all proteins in a defined protein population, rather than investigation of one protein at a time, as in traditional biochemistry. Two major approaches have been described: (1) mass spectrometry-based approaches and (2) protein micro-array approaches. The purpose of this Science Watch article is to describe the fundamental features of these two approaches and to speculate on how proteomics will be useful in nephrology and nephrology research in the coming years.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2005

First analysis of the proteome in two nematomorph species, Paragordius tricuspidatus (Chordodidae) and Spinochordodes tellinii (Spinochordodidae).

The proteome of most parasite species is currently unknown. Hairworms (Nematomorpha), 300 species distributed around the world, are parasitic in arthropods (mainly terrestrial species) when juveniles, but they are free-living in aquatic environments when adult. Most aspects of their systematics and biology are currently unknown. The aim of this paper was (i) to report a novel and reproducible protocol for the analysis of the proteome of hairworms using two-dimensional gel electrophoresis (2-DGE) and mass spectrometry (matrix laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)) and (ii) to determine the level of proteomic divergence between two sympatric but taxonomically unrelated nematomorph species in the adult stage, Paragordius tricuspidatus Dufour (Nematomorpha, Gordiidae) and Spinochordodes tellinii Camerano (Nematomorpha, Gordiidae). In total, 689 protein spots were observed for P. tricuspidatus, 575 for S. tellinii. Only 36.2% spots were shared between the two species. Quantitative analysis of the proteins which are common to both parasite species reveals substantial differences in the pattern of protein expression. These results suggest a rapid evolutionary divergence between these two nematomorph families. Also, to test the value of our MALDI-TOF protocol, we used Actin-2 (Act-2), a protein highly conserved in the course of evolution. Peptide mass fingerprint (PMF) data obtained for Act-2 of P. tricuspidatus and S. tellinii suggest a very high homology with Act-2 of different worms species belonging to the Bilateria phylum (Annelida and Nematoda) and more specifically to Lumbricus terrestris (Annelida, Lumbricidae) and Caenorhabditis elegans (Nematoda, Rhabditidae). We discuss our results in relationship with current ideas concerning the use of proteomics in systematics.

Animals↗