Bacterial peptides are intensively present throughout the human proteome

Trost, Brett; Kusalik, Anthony; Lucchese, Guglielmo; Kanduc, Darja

doi:10.4161/self.1.1.9588

Cited by 30 publications

(25 citation statements)

References 34 publications

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“…We are applying the tool to examine whether exposure to human commensals alters subsequent T cell responses to common human pathogens and to re-examine prevailing paradigms related to autoreactive T cells. This approach, in which we define a T cell epitope based on a well-established T cell epitope-mapping algorithm, 42 , 43 is significantly different from previous analyses 44 . JanusMatrix compares putative T cell epitopes and their TCR-facing residues across genome sequences rather than linear peptide fragments.…”

Section: Discussionmentioning

confidence: 99%

The two-faced T cell epitope

Moise

Gutiérrez

Bailey‐Kellogg

et al. 2013

Human Vaccines & Immunotherapeutics

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Advances in the field of T cell immunology have contributed to the understanding that cross-reactivity is an intrinsic characteristic of the T cell receptor (TCR), and that each TCR can potentially interact with many different T cell epitopes. To better define the potential for TCR cross-reactivity between epitopes derived from the human genome, the human microbiome, and human pathogens, we developed a new immunoinformatics tool, JanusMatrix, that represents an extension of the validated T cell epitope mapping tool, EpiMatrix. Initial explorations, summarized in this synopsis, have uncovered what appear to be important differences in the TCR cross-reactivity of selected regulatory and effector T cell epitopes with other epitopes in the human genome, human microbiome, and selected human pathogens. In addition to exploring the T cell epitope relationships between human self, commensal and pathogen, JanusMatrix may also be useful to explore some aspects of heterologous immunity and to examine T cell epitope relatedness between pathogens to which humans are exposed (Dengue serotypes, or HCV and Influenza, for example). In Hand-Foot-Mouth disease (HFMD) for example, extensive enterovirus and human microbiome cross-reactivity (and limited cross-reactivity with the human genome) seemingly predicts immunodominance. In contrast, more extensive cross-reactivity with proteins contained in the human genome as compared to the human microbiome was observed for selected Treg epitopes. While it may be impossible to predict all immune response influences, the availability of sequence data from the human genome, the human microbiome, and an array of human pathogens and vaccines has made computationally–driven exploration of the effects of T cell epitope cross-reactivity now possible. This is the first description of JanusMatrix, an algorithm that assesses TCR cross-reactivity that may contribute to a means of predicting the phenotype of T cells responding to selected T cell epitopes. Whether used for explorations of T cell phenotype or for evaluating cross-conservation between related viral strains at the TCR face of viral epitopes, further JanusMatrix studies may contribute to developing safer, more effective vaccines.

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Section: Discussionmentioning

confidence: 99%

The two-faced T cell epitope

Moise

Gutiérrez

Bailey‐Kellogg

et al. 2013

Human Vaccines & Immunotherapeutics

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“…In studying the molecular mechanism underlying B. pertussis infection and SD, we have already defined massive peptide sharing between B. pertussis proteome and H. sapiens proteomes [34,35]. Here, we analyzed the bacterial peptide overlap with human proteins linked to SD.…”

Section: Discussionmentioning

confidence: 98%

“…was used to search for exact pentapeptide matches to SD-associated proteins [34,35]. B. pertussis (NCBI taxonomic identifier: 520; strain Tohama 1 [104]) proteome was downloaded from Integr8 [49,105], and, at the time of analysis, contained 3260 proteins for a total of 1,038,965 aa.…”

Section: Methodsmentioning

confidence: 99%

“…Microbial proteomes massively overlap human proteins [34][35][36][68][69][70] in a tight network of metabolic interactions that may carry pathologic sequelae in the host. Indeed, bacterial organisms may interfere with the apoptotic apparatus [71], manipulate and subvert host-cell pathways [72], and interfere with the host immune system and mechanisms [73].…”

Section: Conclusion and Future Perspectivementioning

confidence: 99%

“…In general, microbial-versushuman cross-reactions are expected phenomena in infections. Indeed, numerous reports highlight a high level of microbial-versus-human peptide overlap [34][35][36], and B. pertussis is no exception. In fact, it was found that the number of B. pertussis pentapeptide occurrences in the human proteome (including multiple occurrences) is 6,271,766, with 35,998 human proteins involved in the pentapeptide overlap [35].…”

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confidence: 97%

See 2 more Smart Citations

Peptide Sharing between Bordetella Pertussis Proteome and Human Sudden Death Proteins: A Hypothesis for a Causal Link

Capone

Kanduc

2013

Future Microbiol.

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In vitro genotoxicological evaluation of protein‐rich powder derived fromXanthobactersp.SoF1

Klinzing,

Aabrandt Søndergaard,

Chirom

et al. 2024

J of Applied Toxicology

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One way of limiting the environmental impact of food production and improving food security is to replace part of the animal‐ or plant‐based protein in the human diet with protein sourced from microorganisms. The recently discovered bacterium Xanthobacter sp. SoF1 (VTT‐E‐193585) grows autotrophically using carbon dioxide gas as the only carbon source, yielding protein‐rich biomass that can be processed further into a powder and incorporated into various food products. Since the safety of this microbial protein powder for human consumption had not been previously assessed, its genotoxic potential was evaluated employing three internationally recognized and standardized studies: a bacterial reverse mutation test, an in vitro chromosomal aberration assay in human lymphocytes, and an in vitro micronucleus test in human lymphocytes. No biologically relevant evidence of genotoxicity or mutagenicity was found.

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Bacterial peptides are intensively present throughout the human proteome

Cited by 30 publications

References 34 publications

The two-faced T cell epitope

The two-faced T cell epitope

Peptide Sharing between Bordetella Pertussis Proteome and Human Sudden Death Proteins: A Hypothesis for a Causal Link

In vitro genotoxicological evaluation of protein‐rich powder derived fromXanthobactersp.SoF1

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