Hi-Jack: a novel computational framework for pathway-based inference of host-pathogen interactions

Bioinformatics
Dimitrios KleftogiannisPanos Kalnis

Abstract

Pathogens infect their host and hijack the host machinery to produce more progeny pathogens. Obligate intracellular pathogens, in particular, require resources of the host to replicate. Therefore, infections by these pathogens lead to alterations in the metabolism of the host, shifting in favor of pathogen protein production. Some computational identification of mechanisms of host-pathogen interactions have been proposed, but it seems the problem has yet to be approached from the metabolite-hijacking angle. We propose a novel computational framework, Hi-Jack, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking. Hi-Jack searches metabolic network data from hosts and pathogens, and identifies candidate reactions where hijacking occurs. A novel scoring function ranks candidate hijacked reactions and identifies pathways in the host that interact with pathways in the pathogen, as well as the associated frequent hijacked metabolites. We also describe host-pathogen interaction principles that can be used in the future for subsequent studies. Our case study on Mycobacterium tuberculosis (Mtb) revealed pathways in human-e.g. carbohydrate metabolism, lipids metabolism and...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·P D KarpA Pellegrini-Toole
Aug 3, 2001·Nature Reviews. Molecular Cell Biology·D G Russell
Feb 28, 2002·Trends in Microbiology·Jean Pieters, John Gatfield
Mar 27, 2003·Molecular Microbiology·Christopher M SassettiEric J Rubin
Dec 19, 2003·Nucleic Acids Research·Christian LemerShoshana J Wodak
Jun 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jyothi RengarajanEric J Rubin
Jun 28, 2005·Nucleic Acids Research·Didier CroesJacques van Helden
Oct 11, 2005·Computational Biology and Chemistry·Sharmila AnishettyGautam Pennathur
Dec 13, 2005·Journal of Molecular Biology·Didier CroesJacques van Helden
Mar 4, 2008·Microbiology·Michael Niederweis
Jun 11, 2008·BMC Bioinformatics·Xiong LiuJiang Qian
Mar 14, 2009·Journal of Molecular Biology·Karoline FaustJacques van Helden
Apr 30, 2009·Nucleic Acids Research·Chih-Hung ChouHsien-Da Huang
Apr 1, 2011·Bioinformatics·Deguo XiaKai Zhao
Mar 28, 2013·BMC Bioinformatics·Tomer AltmanPeter D Karp
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Hufeng ZhouLimsoon Wong
Oct 8, 2013·PLoS Computational Biology·Francisco Martínez-JiménezMarc A Marti-Renom
Apr 11, 2014·International Journal of Evolutionary Biology·Asad AmirMohd Asif Siddiqui

❮ Previous
Next ❯

Citations

Feb 18, 2016·Omics : a Journal of Integrative Biology·Luka CulibrkScott J Tebbutt
Sep 22, 2015·Journal of Bioinformatics and Computational Biology·Edgar D CoelhoJosé Luís Oliveira
Oct 7, 2015·Frontiers in Genetics·Konstantinos A TheofilatosSeferina Mavroudi

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

The Journal of Biological Chemistry
Bernard L Horecker
Nihon rinsho. Japanese journal of clinical medicine
Z Kizaki, T Sawada
© 2022 Meta ULC. All rights reserved