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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:21245
039 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