=Paper=
{{Paper
|id=Vol-2931/ICBO_2019_paper_41
|storemode=property
|title=Ontological Modeling of Two-Component Regulatory Systems
|pdfUrl=https://ceur-ws.org/Vol-2931/ICBO_2019_paper_41.pdf
|volume=Vol-2931
|authors=Hsin-Hui Huang,Meng Liu,Yongqun He
|dblpUrl=https://dblp.org/rec/conf/icbo/HuangLH19
}}
==Ontological Modeling of Two-Component Regulatory Systems==
https://ceur-ws.org/Vol-2931/ICBO_2019_paper_41.pdf
Ontological Modeling of Two-Component Regulatory Systems
Hsin-Hui Huanga,c, Meng Liub, Yongqun Hec
a
Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
b
State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai,
China
c
University of Michigan Medical School, Ann Arbor, MI 48109, USA
Abstract (BFO). The PhoPQ TCS is a common TCS as shown in many
bacteria such as E. coli. PhoPQ TCS is essential for mediateing
The two-component regulatory systems (TCSs), which comprise a the adaptation to magnesism limiting condition, stress resistance,
sensor kinase and a response regulator, serve as a prevalent and virulence (3). The PhoPQ includes a sensor protein PhoQ and
signal transduction system involving in multiple behaviors. To a response regulator PhoP (Fig 1).
support systematic and interoperable representatoin of various
types of TCS, we have initiated the development of a community-
based Ontology of Two-Component Systems (OTCS). Bacterial
PhoPQ TCS in Escherichia coli is used as an example TCS for
OTCS modeling in the study.
Figure. 1. Example of bacterial TCS
Keywords: More information are also added in OTCS. For example, the
OTCS, Two-component regulatory system, Ontology genes that encoded TCS proteins are also represented in OTCS.
OTCS also defines different roles, such as ‘bacterial sensor role’
Introduction that inheres in TCS sensor proteins. As a widely used bacterial
model, E. coli includes 30 TCSs. These TCSs, the TCS stimuli,
TCS is one of the well-known signal transduction system and and the TCS effector protein are first represented in OTCS. TCSs
exists among in nearly all prokaryotes, many Archaea, and in other bacteria are also being added to OTCS. We will also
eukaryotes such as plants, fungi, and yeasts (1). In general, the evaluate how OTCS can be used to support TCS comparisons and
TCS consists of two proteins, a sensor kinase for sensing signals knowledge discovery. The OTCS project website is located at
and a response regulator that affects the nurmous cellular GitHub:https://github.com/biomedontology/otcs.
regulatory circuits. TCSs play a critical role in regulating
virulence, antibiotic resistance, and adaptation (2). However, the Conclusions
signals and cellular response of the TCSs are complicated. To
better understand TCSs, we initiated our development of the We have initiated the development of the OTCS to support
community-driven Ontology of Two-Component Systems systematic and logic representation of TCS with the aim to not
(OTCS) to represent and integrate various relationships among
only integrate the knowledge of TCS but also systematically
TCSs, signals, TCSs regulon, and regulons’ role.
elucidate the TCSs regulatory network.
Methods Acknowledgements
The OTCS ontology design follows the Open Biomedical This work was supported by grant 108-2917-I-010-001 from Min-
Ontologies (OBO) Foundry principle, and aligns with and reuses istry of Science and Technology of Taiwan.
terms from the OBO ontology such as the Protein Ontology (PR)
and the Ontology of Genes and Genomes (OGG). Protégé 4.3 References
OWL ontology editor (http:// protege.stanford.edu/) was used for
ontology establishment. Ontofox (http://ontofox.hegroup.org/)
1. Stock AM, Robinson VL, Goudreau PN. Two-component sig-
was used to obtain the related term from different ontologies.
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2. Gotoh Y, Eguchi Y, Watanabe T, Okamoto S, Doi A, Utsumi
Results R. Two-component signal transduction as potential drug targets
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The OTCS key term ‘two-component regulatory system’ 3. Yuan J, Jin F, Glatter T, Sourjik V. Osmosensing by the bacte-
(OTCS_0000001) is defined as a subclass of RO:system, which rial PhoQ/PhoP two-component system. Pron Natl Acad Sci U S
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