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 of proteins, for example, the uninvestigated GGDEF domain proteins.

1 Results and Analysis
1.1 The protein sequence characteristics of Xcc 8004 containing GGDEF domain
According to the sequence alignment, the homology in the overall amino acid sequences containing the GGDEF domain in Xcc 8004 is very low. And the sequence conservation is not high as the the other species based on the phylogenetic tree (Figure 1), which may associate with the functional diversity of the GGDEF domain proteins.

Figure 1 Phylogenetic tree of GGDEF domain proteins of Xcc 8004

1.2 The domain architecture characteristics of Xcc 8004 containing GGDEF domain
In order to gain more relatively bioinformatics information on these proteins, we analyze the domain architecture of them. The domain architecture is defined as the sequential order of the domains in a protein, and the common domain architecture is defined as the architecture shared by more than two proteins. Both these architectures provide important information sources for studying proteins and their functions (Geer et al., 2002; Nikolskaya et al., 2007; Paliakasis et al., 2008; Byungwook and Doheon, 2009). We used the Pfam (Finn et al., 2010) and SMART (Letunic et al., 2009) websites to search the protein sequence of Xcc 8004. The results showed that there were 32 proteins containing GGDEF domains in Xcc 8004. Function of these proteins were diverse according the previous reports (Ryan et al., 2007; Ryan et al., 2010; Ryan and Dow, 2010; Mao et al., 2011), which allowed us to analyze the domain architecture of the proteins using bioinformatics web services.

1.2.1 Domain architecture of GGDEF domain proteins involved in virulence in Xcc 8004
Ryan et al (2007) found 9 mutants with GGDEF domain proteins were involved in pathogenesis in Xcc 8004 by assay the virulence capability of all mutants with single-gene disruption. We compared the domain architecture of the proteins encoded by XC_0249, XC_0420, XC_0637, XC_0831, XC_1036, XC_1476, XC_1582, XC_1841 and XC_2324 (Figure 2). The results showed that these 9 proteins share little common domain architecture except XC_1476 and XC_2324, which shared the PAS_4-GGDEF-EAL architecture. These 8 specific domain architectures with GGDEF domain proteins involved in virulence in Xcc 8004. Although these proteins were almost different at the level of global domain architecture, some of them indeed shared common domain architecture based on local comparison. We found that the proteins encoded by XC_1476, XC_2324, XC_1582 and XC_1841 containing the GGDEF-EAL, whereas XC_1476, XC_2324 and XC_637 all contained PAS_4-GGDEF.

Figure 2 The domain architectures of GGDEF domain proteins involved in virulence of Xcc 8004

 
Data analysis of other reports also found that the PAS_4-GGDEF was common domain architecture in the GGDEF domain proteins associated with pathogenesis. Mao et al (2011) assayed the virulence of GGDEF and EAL domain gene mutants using an alternative experimental procedure instead of that in Ryan et al (2007) used previously, the strains with a single gene mutation in XC_637, XC_1036, XC_1476, XC_2226, XC_2324 and XC_4313 were tested under different conditions of illumination. The domain architectures in GGDEF domain protein which involved in enhancing virulence of Xcc under strong light were compared. The results indicated these three proteins encoded by XC_1476, XC_2324 and XC_3829 respectively shared the common domain, PAS_4-GGDEF. Whereas the protein which had the architecture of PAS-GGDEF encoded by XC_1036 played a role in enhancing virulence of Xcc under weak light (Figure 3). To our knowledge, PAS_4-GGDEF was the first common domain architecture that participated in enhancing virulence of Xcc in response to strong light.

Figure 3 Comparison of domain architecture of GGDEF domain protein involved in enhancing virulence of Xcc in response to light intensity

1.2.2 Domain architecture in GGDEF domain proteins involved in the production of extracellular enzyme in Xcc 8004
Ryan et al (2007) assayed the enzyme production ability of all the mutants of Xcc 8004 containing the GGDEF domain proteins. The results indicated that 7 GGDEF domain proteins encoded by XC_637, XC_2228, XC_2275, XC_2276, XC_1582, XC_1841 and XC_3829 were found to be involved in the production of endoglucanase, major extracellular enzymes (Figure 4). And we analyzed the domain architecture. The result revealed that none of them had a common architecture but some of them shared the common structural elements, based on local comparison that the domain architectures, f PAS_4-GGDEF and PAS_4-PAS_4, which were in both of the proteins encoded by XC_637 and XC_3829; GGDEF-EAL contained by the protein encoded by XC_2228, XC_2276, XC_1582 and XC_1841 (Figure 4).

Figure 4 Domain architecture of GGDEF domain proteins involved in endoglucanase production in Xcc 8004

1.2.3 Domain architecture of GGDEF domain proteins involved in biofilm formation in Xcc 8004
Ryan et al (2007) assayed the formation ability of biofilm in GGDEF mutations, the results indicated that only 2 GGDEF domain proteins encoded by XC_2161 and XC_2324 respectively were found to be involved in biofilm formation in Xcc 8004. While we analyzed the domain architectures of both of them, the results revealed that both these proteins shared neither common nor local common domain architecture (Figure 5). A2M-comp domain was found between GGDEF and EAL domain in XC_2161-encoding protein, whereas GGDEF domain was shown adjacent to EAL domain in the protein coded by XC_2324 (Figure 5).

Figure 5 Domain architecture of GGDEF domain proteins involved in biofilm formation in Xcc 8004

1.2.4 Domain architecture of GGDEF domain proteins involved in motility in Xcc 8004
Ryan et al (2007) assayed the motorial ability of the mutant GGEDE proteins, the results revealed that 2 GGDEF domain proteins encoded by XC_2161 and XC_2226 respectively were found to be related to motility in Xcc 8004. The 2 proteins were differed in their common or local common domain architectures from our domain architecture analysis (Figure 6). The architecture of PAS_3-PAS_4-PAS_3 in XC_2226-encoding protein was not found in the protein coded by XC_2161. And the EAL domain follows the GGDEF domain in the protein encoded by XC_2226, which was also different from the domain arrange of XC_2161-encoding protein.

Figure 6 Domain architecture of GGDEF domain proteins involved in mobility in Xcc 8004

2 Discussion
The domain architecture analysis showed that the interesting profile in the GGDEF domain proteins functioning differently in Xanthomonas campestris, such as, PAS_4-GGDEF, GGDEF-EAL and PAS_4-GGDEF-EAL were shared by the proteins which were found to be involved in virulence; and PAS_4-PAS_4, PAS_4-GGDEF and GGDEF-EAL were shared by the proteins which involved in the production of endoglucanase. The functions of the proteins with the GGDEF domain, PAS domain or EAL domains in large number of bacteria remains unknown, and the proteins with these domains were reported playing important roles in essential cell processes (Seshasayee et al., 2010). So, the results provided some important information to prediction the function of these proteins containing GGDEF domain, PAS domain including PAS_4, PAS and PAS_3 members (Hao et al., 2011), or EAL domain. The results were benefit for the plant disease research as they gave some clues of structural characteristics to the proteins involved in virulence, and also to hypothetical proteins (Nikolskaya et al., 2007). Not similar to any protein known at sequence level, the functions of the proteins with GGDEF domain were hard to be predicted.

The knowledge for domain architectures of the proteins functioning differently in Xanthomonas campestris should not be limited in our report because this research only based on few functions of Xcc 8004. Many new characteristics may be drawn from domain architecture of GGDEF domain proteins in other Xcc strains, for example, strain Xc17, containing Xcc 1294, the homologous gene with XC_2946, and Xcc 2731, homologous gene with XC_1383 in Xcc 8004. All of them participated in the cell adhesion according to the reports of Hsiao et al (2011a; 2011b). Strain XC1, containing ravR/Xcc1958, homologous gene with XC_2228 in Xcc 8004. This stain involved in extracellular polysaccharide and proteinase production (He et al., 2009).

3 Materials and Methods
3.1 Data sources
The protein sequences of Xcc 8004 were downloaded from the database in NCBI (http://www.ncbi.nlm.nih.gov/genome). The GenBank accession No. of Xcc 8004 is NC_007086.

3.2 Identification of domain
By using the Pfam database (http://pfam.sanger.ac.uk/), we searched the information of protein families and domains which was constructed by the Hide Markov Models. The SMART website (http://smart.embl-heidelberg.de/), a simple modular architecture research tool, providing the service for searching and annotation of domain also can be used. We uploaded the protein sequence documents, products of all genes, to the website of Pfam to search batch domains to obtain the annotation of all proteins. Using string “GGDEF domain”, we could search the proteins containing GGDEF domain, which could be analyzed via SMART, and gained the information of proteins.

3.3 Protein or domain annotation resources
The experimental evidences and annotation related to the functions of the proteins or domains were obtained from the papers previously reported (Ryjenkov et al., 2005; Seshasayee et al., 2010; Hao et al 2011), and from the pfam and SMART web services.

Authors' contributions
Suisheng Zhang involved in the data analyses and writing, who was the correspondence author of this paper. Wei Jiang and Yanhua Yu involved in data collection and analyses, and modified the paper. All authors have read and approved the final manuscript.

Acknowledgments
This work was supported by grant from Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering (J0803). And we thank the faculties of State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Key Laboratory of Biorefinery in Guangxi Academy of Sciences and Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering for their useful suggestion.

Reference
Byungwook L., and Doheon L., 2009, Protein comparison at the domain architecture level, BMC Bioinformatics, 10(Suppl 15): S5
http://dx.doi.org/10.1186/1471-2105-10-S15-S5
PMid:19958515    PMCid:2788356

Finn R.D., Mistry J., Tate J., Coggill P., Heger A., Pollington J.E., Gavin O.L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E.L., Eddy S.R., and Bateman A., 2010, The pfam protein families database, Nucleic Acids Research, 38(Database issue): D211-22
http://dx.doi.org/10.1093/nar/gkp985

Geer L.Y., Domrachev M., Lipman D.J., and Bryant S.H., 2002, Cdart: protein homology by domain architecture, Genome Research, 12(10): 1619-1623
http://dx.doi.org/10.1101/gr.278202
PMid:12368255    PMCid:187533

Hao N., Whitelaw M.L., Shearwin K.E., Dodd I.B., and Chapman-smith A., 2011, Identification of residues in the n-terminal pas domains important for dimerization of arnt and ahr, Nucleic Acids Research, 39(9): 3695-3709
http://dx.doi.org/10.1093/nar/gkq1336
PMid:21245039    PMCid:3089468

He Y.Q., Zhang L., Jiang B.L., Zhang Z.C., Xu R.Q., Tang D.J., Qin J., Jiang W., Zhang X., Liao J., Cao J.R., Zhang S.S., Wei M.L., Liang X.X., Lu G.T., Feng J.X., Chen B., Cheng J., and Tang J.L., 2007, Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris, Genome Biology, 8(10): R218
http://dx.doi.org/10.1186/gb-2007-8-10-r218
PMid:17927820    PMCid:2246292

He Y.W., Boon C., Zhou L., and Zhang L.H., 2009, Co-regulation of Xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system ravs/ravr, Molecular Microbiology, 71(6): 1464-1476
http://dx.doi.org/10.1111/j.1365-2958.2009.06617.x
PMid:19220743

Hsiao Y.M., Liu Y.F., Fang M.C., and Song W.L., 2011b, Xcc2731, a GGDEF domain protein in Xanthomonas campestris, is involved in bacterial attachment and is positively regulated by clp, Microbiological Research, 166(7): 548-565
http://dx.doi.org/10.1016/j.micres.2010.11.003
PMid:21237626

Hsiao Y.M., Song W.L., and Liao C.T., Lin I.H., Pan M.Y., and Lin C.F., 2011a, Transcriptional analysis and functional characterization of xcc1294 gene encoding a GGDEF domain protein in Xanthomonas campestris pv. Campestris, Archives of Microbiology, doi: 10.1007/s00203.011.0760.3
http://dx.doi.org/10.1007/s00203.011.0760.3
PMid:22002465

Letunic I., Doerks T., and Bork P., 2009, Smart 6: recent updates and new developments, Nucleic Acids Research, 37(Database issue): D229-232
http://dx.doi.org/10.1093/nar/gkn808
PMid:18978020    PMCid:2686533

Mao D., Luo T., Li C., Luo C., Zheng L., and He C., 2011, Light signaling mediated by pas domain-containing proteins in Xanthomonas campestris pv. campestris, FEMS Microbiology Letters, doi: 10.1111/j.1574-6968.2011.02426.x
http://dx.doi.org/10.1111/j.1574-6968.2011.02426.x
PMid:22029486

McWilliam H., Valentin F., Goujon M., Li W., Narayanasamy M., Martin J., Miyar T., and Lopez R., 2009, Web services at the european bioinformatics institute, Nucleic Acids Research, 37(Web Server issue): W6-10 doi: 10.1093/nar/gkp302

Navarro M.V., De N., Bae N., Wang Q., and Sondermann H., 2009, Structural analysis of the ggdef-eal domain-containing c-di-gmp receptor fimx, Structure, 17(8): 1104-1116
http://dx.doi.org/10.1016/j.str.2009.06.010
PMid:19679088    PMCid:2747306

Nikolskaya A.N., Arighi C.N., Huang H., Barker W.C., and Wu C.H., 2007, Pirsf family classification system for protein functional and evolutionary analysis, Evolutionary Bioinformatics Online, 2: 197-209
PMid:19455212    PMCid:2674652

Paliakasis C.D., Michalopoulos I., and Kossida S., 2008, Web-based tools for protein classification, Methods in Molecular Biology, 428: 349-367
http://dx.doi.org/10.1007/978-1-59745-117-8_18

Qian W., Jia Y., Ren S.X., He Y.Q., Feng J.X., Lu L.F., Sun Q., Ying G., Tang D.J., Tang H., Wu W., Hao P., Wang L., Jiang B.L., Zeng S., Gu W.Y., Lu G., Rong L., Tian Y., Yao Z., Fu G., Chen B., Fang R., Qiang B., Chen Z., Zhao G.P., Tang J.L., and He C., 2005, Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris, Genome Research, 15(6): 757-767
http://dx.doi.org/10.1101/gr.3378705
PMid:15899963    PMCid:1142466

Ryan R.P., and Dow J.M., 2010, Intermolecular interactions between hd-gyp and ggdef domain proteins mediate virulence-related signal transduction in Xanthomonas campestris, Virulence, 1(5): 404-408
http://dx.doi.org/10.4161/viru.1.5.12704
PMid:21178479

Ryan R.P., Fouhy Y., Lucey J.F., Jiang B.L., He Y.Q., Feng J.X., Tang J.L., and Dow J.M., 2007, Cyclic di-gmp signalling in the virulence and environmental adaptation of Xanthomonas campestris, Molecular Microbiology, 63(2): 429-442
http://dx.doi.org/10.1111/j.1365-2958.2006.05531.x
PMid:17241199

Ryan R.P., Mccarthy Y., Andrade M., Farah C.S., Armitage J.P., and Dow J.M., 2010, Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris, Proceedings of the National Academy of Sciences of the United States of America, 107(13): 5989-5994
http://dx.doi.org/10.1073/pnas.0912839107
PMid:20231439    PMCid:2851925

Ryjenkov D.A., Tarutina M., Moskvin O.V., and Gomelsky M., 2005, Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain, The Journal of Bacteriology, 187(5): 1792-1798
http://dx.doi.org/10.1128/JB.187.5.1792-1798.2005
PMid:15716451    PMCid:1064016

Seshasayee A.S., Fraser G.M., and Luscombe N.M., 2010, Comparative genomics of cyclic-di-gmp signalling in bacteria: post-translational regulation and catalytic activity, Nucleic Acids Research, 38(18): 5970
http://dx.doi.org/10.1093/nar/gkq382
PMid:20483912    PMCid:2952852