Download A7: Decoding genome encoded host-pathogen

A7: Decoding genome encoded host-pathogen protein interactions and response
networks involved in c-di-GMP signalling
Akash Ranjan, Centre for DNA Fingerprinting and Diagnostics (CDFD)
State of the art: The discovery of c-di-GMP as a universal secondary messenger is a
breakthrough in bacterial physiology: high concentrations activate sessility, adhesion, biofilm
and cell cycle progression; low concentrations stimulate single cell dispersal, motility and upregulation of virulence genes (1-3). GGDEF domain proteins synthesize ci-di-GMP, EAL or
HD-GYP domain containing proteins degrade it. These domain containing proteins are
abundant and often modular in a diverse set of bacteria, i.e. containing additional domains
such as PilZ, REC, PAS etc. (4). The modular nature enables participation in various
biological processes, their diverse distribution in various species probably helps in niche
adaptation. Our analysis will unravel their functional relations and organizational principles.
Previous work: We have identified GGDEF, EAL, HD and PilZ domain containing 16179
proteins in 779 completely sequenced bacterial genomes. We found that these domains cooccur with 124 other domains, which suggests their contribution in many biological
processes. We also mapped their sequential order along 16179 proteins often termed
domain architecture or organization. A directed graph was constructed by linking domains
located adjacent to each other from N- to C- terminal order, analyzing the c-di-GMP
associated functional patterns (5), now an automated process. We are in the process of
proposing a new protein-protein interaction prediction method using five genomic context
methods and gene expression profiling in various conditions (6, 7). With this template we will
extend the domain work to identify their interacting partners (8).
Working hypothesis and work plan: Preliminary analysis of the GGDEF, EAL, HD-GYP
and PilZ domain containing proteins suggested that the abundance of these domains is for
functional diversity. We hypothesize a correlation of the variable number of these domains in
various species and their specific phenotype/habitat, their co-occurrence with functionally
diverse domains may be responsible for sensing environmental cues, causing appropriate
physiological adaptations. Can we identify the common domain usage pattern and probable
response they generate? What are the effectors to which c-di-GMP can bind? Through
available microarray data and protein-protein interaction networks we can identify the
functional modules to which different GGDEF and EAL domain containing proteins belong.
Comparison of domains present in pathogenic vs. non-pathogenic organisms can provide the
pathogenesis related c-di-GMP signalling modules, leading to the identification of proteins
exclusively present in pathogenic organisms. The second aspect will be to identify the
probable interacting partners of these proteins based on integrated analysis protein-protein
interaction networks and microarray datasets, providing us with probable pathways affected
by c-di-GMP signalling.
Proposed thesis topics: (1) Reconstruction of a genome-wide protein-protein functional
linkage map of E. coli: A computational approach to study cellular physiology associated with
c-di-GMP signalling; (2) Functional characterization of molecular interactions involved in c-diGMP signalling.
Interlinkage: Our bioinformatics analysis will be experimentally confirmed by. R. Hengge
(A2). We will send a student from our lab to the lab of R. Hengge, and receive a student from
the Berlin. We will also assist L.H. Wieler and C. Ewers (A1) with bioinformatics analyses.
References: (1) Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263-73 (2) Jenal U, J
Malone (2006) Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40: 385-407 (3) Pesavento C et al. (2008)
Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev 22:2434-46 (4) Romling
U, M Gomelsky, MY Galperin (2005) C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 57:629-39 (5)
Kummerfeld SK, SA Teichmann (2009) Protein domain organisation: adding order. BMC Bioinformatics 10: 39 (6) Harrington
ED, LJ Jensen, P Bork (2008) Predicting biological networks from genomic data. FEBS Lett 582:1251-8 (7) von Mering C, et al.
(2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403. (8) Pujana MA, et
al.(2007) Network modelling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39:1338-49.