Page 4 - Molecular Pathogens

Molecular Pathogens 2012, Vol.3, No.1, 1-5
http://mp.sophiapublisher.com
1
Research Report Open Access
In silico Analysis of GGDEF Domain Proteins Functioning Differently in
Xanthomonas campestris
Suisheng Zhang1 , Wei Jiang2 , Yanhua Yu2
1. State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory
of Biorefinery, Guangxi Academy of Sciences, Nanning, 530007, P.R. China
2. Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, Nanning,
530004, P.R. China
Corresponding authors email: zss99@vip.163.com; Authors
Molecular Pathogens, 2012, Vol.3, No.1 doi: 10.5376/mp.2012.03.0001
Received: 11 Dec., 2011
Accepted: 17 Jan., 2012
Published: 20 Jan., 2012
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative
Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Zhang et al., 2012, In silico Analysis of GGDEF Domain Proteins Functioning Differently in Xanthomonas campestris, Molecular Pathogens, Vol.3, No.1 1-5 (doi:
10.5376/mp.2012.03.0001)
Abstract It has been reported that GGDEF domain proteins, containing five conserve amino acid residues with two glycines (G),
one aspartic acid (D), one glutamic acid (E), and one phenylalanine (F) respectively, played key roles in the essential cell process of
signal transduction, growth and pathogenicity. There are 32 GGDEF domain proteins were predicted in Xanthomonas campestris pv.
campestris str. 8004 (Xcc 8004). And several of them were involved in the different cell processes of pathogenicity, production of
extracellular enzyme, formation of biofilm and motility according to the experimental evidence. In this work, we analyzed the GGDEF
domain proteins functioning differently in Xcc using bioinformatics web services, and focused on the analysis of the domain
architectures. The results revealed that the overall domain architectures of these proteins were almost different except the
PAS_4-GGDEF-EAL, which distributed in the proteins associated with virulence. According to the local comparison among the
proteinic structures, the common domain architectures were found in the proteins involved in pathogenicity, including PAS_4-GGDEF
and GGDEF-EAL. The PAS_4-PAS_4, PAS_4-GGDEF, and GGDEF-EAL in the proteins were involved in the production of
endoglucanase in Xcc. The results of this research would provide some clues for inferring the function of proteins with GGDEF
domain.
Keywords Xanthomonas campestris pv. campestris; GGDEF; Domain architecture; In silico analysis
Background
Recently, GGDEF domain proteins, which were
identified in most bacterial species, are the key
molecules involved in the essential cellular processes,
including signal transduction, transcription regulation,
biofilm formation, and mobility (Ryjenkov et al., 2005;
Navarro et al., 2009; Mao et al., 2011). Currently, our
knowledge of GGDEF domain proteins are needed to
be further because previous reports on function of the
proteins are still confined on the experimental
evidences from model bacteria researches. For example,
there are 32 GGDEF domain-containing proteins in
Xcc 8004, an important model phytopathogen (Qian et
al., 2005; He et al., 2007). Some of the proteins in this
model had been experimentally verified that they
participated in the key cellular processes in Xcc 8004,
including pathogenicity, extracellular enzyme production,
biofilm formation and mobility (Ryan et al., 2007;
Ryan et al., 2010; Ryan and Dow, 2010; Mao et al.,
2011). The results provided references for the functional
researches of these proteins in other species, and
paved the way for studying the function of the
proteins with the DDGEF domain.
In silico analysis of protein can assist in inferring the
function of a specific protein, which has been
demonstrated in various studies, and is being developed
with increasing bioinformatics resources (McWilliam
et al., 2009; Byungwook and Doheon, 2009). In this
research, we analyzed the GGDEF domain proteins
functioning differently in Xcc 8004, and inferred the
relationship of structures and functions of the proteins
with the bioinformatics web services. The results
should pave the way for successful function prediction