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Pathogens
Special Issues
Computational Biology Applied to Host-Pathogen Interactions
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Computational Biology Applied to Host-Pathogen Interactions

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 8862

Special Issue Editors

Dr. Shishir K. Gupta

E-Mail Website
Guest Editor
Department of Bioinformatics, Biozentrum, Universität Würzburg, Am Hubland, D-97074 Wuerzburg, Germany
Interests: host-pathogen interactions; network modelling; comparative genomics; transcriptomics
Dr. Mugdha Srivastava

E-Mail Website
Guest Editor
Core Unit Systems Medicine, University of Wuerzburg, D-97080 Wuerzburg, Germany
Interests: bioinformatics; metabolic networks; big data analysis
Prof. Dr. Thomas Dandekar

E-Mail Website
Guest Editor
Department of Bioinformatics, Biozentrum, Universität Würzburg, Am Hubland, D-97074 Wuerzburg, Germany
Interests: bioinformatics; infection biology; systems biology; network modelling

Special Issue Information

Dear Colleagues,

As highlighted by the efforts to fight the COVID-19 pandemic, a deeper understanding of the pathophysiology associated with infectious diseases is essential to protect us from current and emerging infections. Attempting to understand immune protection or to identify a new drug target is a challenge, as well as the identification of pathogen proteins that control host cell signalling and metabolism (host reprogramming). In this pursuit, computational approaches provide a rapid solution to study host and pathogen interactions at the system level, to mine and exploit network biology insights. Through the integration of multi-omics data to molecular networks, studies in recent years have identified new potential host and pathogen factors involved in pathogenicity. One of the most important types of molecular networks is host-pathogen interaction (HPI) networks in the study of infectious diseases. Advances in understanding the essence of HPI could shed light on the concepts of mechanisms of infections. Immune defences and important interactions provide an important clue to understand what is happening during an infection. Meticulous validation by experimental data is similarly important and with the advent of large-scale omics data, analysis pipelines become increasingly important. Infection happens and can come from bacteria, viruses, parasites and fungi. From all these domains of life articles involving computational approaches and their validation are invited.

For this Special Issue of Pathogens, we invite you to submit a review or original research article related to host-pathogen interactions. Validation of the approach or the interactions predicted is also important. Potential topics include but are not limited to:

Reconstruction of HPI networks

Analysis of HPI networks

Pathogen targeting host signaling/metabolism

Evolution of pathogenicity

Interactome analysis of pathogen

Modeling or host immune response

We look forward to your contributions.

Dr. Shishir K. Gupta
Dr. Mugdha Srivastava
Prof. Dr. Thomas Dandekar
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • host-pathogen interactions
  • domain-domain interactions
  • interactome
  • interologs
  • drug targets
  • network analysis
  • PPI network

Published Papers (3 papers)

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Research

13 pages, 1724 KiB  
Article
Secretomic Insights into the Pathophysiology of Venturia inaequalis: The Causative Agent of Scab, a Devastating Apple Tree Disease
by Yash Paul Khajuria, Bashir Akhlaq Akhoon, Sanjana Kaul and Manoj Kumar Dhar
Pathogens 2023, 12(1), 66; https://doi.org/10.3390/pathogens12010066 - 31 Dec 2022
Cited by 2 | Viewed by 2059
Abstract
Apple scab, caused by Venturia inaequalis, is one of the world’s most commercially significant apple diseases. The fungi have a catastrophic impact on apples, causing considerable losses in fruit quality and productivity in many apple-growing locations despite numerous control agents. Fungi secrete [...] Read more.
Apple scab, caused by Venturia inaequalis, is one of the world’s most commercially significant apple diseases. The fungi have a catastrophic impact on apples, causing considerable losses in fruit quality and productivity in many apple-growing locations despite numerous control agents. Fungi secrete various effectors and other virulence-associated proteins that suppress or alter the host’s immune system, and several such proteins were discovered in this work. Using state-of-the-art bioinformatics techniques, we examined the V. inaequalis reference genome (EU-B04), resulting in the identification of 647 secreted proteins, of which 328 were classified as small secreted proteins (SSPs), with 76.52% of SSPs identified as anticipated effector proteins. The more prevalent CAZyme proteins were the enzymes engaged in plant cell wall disintegration (targeting pectin and xylanase), adhesion and penetration (Cutinases/acetyl xylan esterase), and reactive oxygen species formation (multicopper oxidases). Furthermore, members of the S9 prolyl oligopeptidase family were identified as the most abundant host defense peptidases. Several known effector proteins were discovered to be expressed during the V. inaequalis infection process on apple leaves. The present study provides valuable data that can be used to develop new strategies for controlling apple scab. Full article
(This article belongs to the Special Issue Computational Biology Applied to Host-Pathogen Interactions)
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22 pages, 4183 KiB  
Article
Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions
by Heidy Elkhaligy, Christian A. Balbin and Jessica Siltberg-Liberles
Pathogens 2022, 11(5), 583; https://doi.org/10.3390/pathogens11050583 - 15 May 2022
Cited by 3 | Viewed by 2120
Abstract
Protein-protein interactions drive functions in eukaryotes that can be described by short linear motifs (SLiMs). Conservation of SLiMs help illuminate functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance due to mutational processes not only [...] Read more.
Protein-protein interactions drive functions in eukaryotes that can be described by short linear motifs (SLiMs). Conservation of SLiMs help illuminate functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance due to mutational processes not only in eukaryotes but also in pathogenic bacteria and viruses. Further, functional eukaryotic SLiMs are often found in disordered regions. Although proteomes from pathogenic bacteria and viruses have less disorder than eukaryotic proteomes, their proteins can successfully mimic eukaryotic SLiMs and disrupt host cellular function. Identifying important SLiMs in pathogens is difficult but essential for understanding potential host-pathogen interactions. We performed a comparative analysis of structural features for experimentally verified SLiMs from the Eukaryotic Linear Motif (ELM) database across viruses, bacteria, and eukaryotes. Our results revealed that many viral SLiMs and specific motifs found across viruses and eukaryotes, such as some glycosylation motifs, have less disorder. Analyzing the disorder and coil properties of equivalent SLiMs from pathogens and eukaryotes revealed that some motifs are more structured in pathogens than their eukaryotic counterparts and vice versa. These results support a varying mechanism of interaction between pathogens and their eukaryotic hosts for some of the same motifs. Full article
(This article belongs to the Special Issue Computational Biology Applied to Host-Pathogen Interactions)
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17 pages, 2330 KiB  
Article
Identification of Salicylic Acid Mechanism against Leaf Blight Disease in Oryza sativa by SR-FTIR Microspectroscopic and Docking Studies
by Wannaporn Thepbandit, Narendra Kumar Papathoti, Jayasimha Rayalu Daddam, Kanjana Thumanu, Supatcharee Siriwong, Toan Le Thanh and Natthiya Buensanteai
Pathogens 2021, 10(6), 652; https://doi.org/10.3390/pathogens10060652 - 24 May 2021
Cited by 13 | Viewed by 3037
Abstract
The present study was to investigate the application and mechanism of salicylic acid (SA) as SA-Ricemate for the control of leaf blight disease using a Synchrotron Radiation-based Fourier-Transform Infra-Red (SR-FTIR) microspectroscopy and docking studies. After treating rice plants cv. KDML 105 with SA-Ricemate, [...] Read more.
The present study was to investigate the application and mechanism of salicylic acid (SA) as SA-Ricemate for the control of leaf blight disease using a Synchrotron Radiation-based Fourier-Transform Infra-Red (SR-FTIR) microspectroscopy and docking studies. After treating rice plants cv. KDML 105 with SA-Ricemate, the leaves were inoculated with Xanthomonas oryzae pv. oryzae, the causal agent of leaf blight, and disease severity were assessed. The leaves were also used to detect changes in endogenous SA content. The results indicated that SA-Ricemate, as an activated compound, reduced disease severity by 60% at three weeks post-inoculation and increased endogenous content by 50%. The SR-FTIR analysis of changes in the mesophyll of leaves (treated and untreated) showed that the groups of lipids, pectins, and proteins amide I and amide II occurred at higher values, and polysaccharides were shown at lower values in treated compared to untreated. Besides, docking studies were used to model a three-dimensional structure for Pathogenesis-related (PR1b) protein and further identify its interaction with SA. The results showed that ASP28, ARG31, LEU32, GLN97, and ALA93 are important residues that have strong hydrogen bonds with SA. The docking results showed that SA has a good interaction, confirming its role in expression. Full article
(This article belongs to the Special Issue Computational Biology Applied to Host-Pathogen Interactions)
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