Computational Molecular Biology
12
XJM, JM and GL analyzed the data and prepared the
manuscript. All authors read and approved the final
manuscript.
Acknowledgments
The work is funded by the Ohio Plant Biotechnology
Consortium [grant 2011-001] (through the Ohio State
University,
Ohio Agricultural
Research and
Development Center),
and Youngstown State
University (YSU) Research Council [grant 2010-2011
and 12-11]. The work is also supported by a YSU
Research Professorship and the College of Science,
Technology, Engineering, and Mathematics Dean’s
reassigned time for research to XJM. JM was
supported with a graduate research assistantship by
the Center for Applied Chemical Biology at YSU.
References
Agrawal G.K., Jwa N.S., Lebrun M.H., Job D., and Rakwal R.,
2010, Plant secretome: unlocking secrets of the secreted
proteins, Proteomics, 10: 799-827
http://dx.doi.org/10.1002/pmic.200900514
Alexandersson E., Ali A., Resjö S., and Andreasson E., 2013,
Plant secretome proteomics, Front. Plant Sci., 4: 9
http://dx.doi.org/10.3389/fpls.2013.00009
Bendtsen J.D., Jensen L.J., Blom N., von Heijne G., and
Brunak S., 2004a, Feature based prediction of
non-classical and leaderless protein secretion, Protein Eng.
Des. Sel., 17: 349-356
http://dx.doi.org/10.1093/protein/gzh037
Bendtsen J.D., Nielsen H., von Heijne G., and Brunak S.,
2004b, Improved prediction of signal peptides: SignalP
3.0, J. Mol. Biol., 340: 783-795
http://dx.doi.org/10.1016/j.jmb.2004.05.028
Blum T., Briesemeister S., and Kohlbacher O., 2009,
MultiLoc2: integrating phylogeny and Gene Ontology
terms improves subcellular protein localization prediction,
BMC Bioinformatics, 10: 274
http://dx.doi.org/10.1186/1471-2105-10-274
Borner G.H., Lilley K.S., Stevens T.J., and Dupree P., 2003,
Identification of glycosylphosphatidylinositol-anchored
proteins in Arabidopsis. A proteomic and genomic analysis,
Plant Physiol., 132: 568-577
http://dx.doi.org/10.1104/pp.103.021170
Borner G.H., Sherrier D.J., Stevens T.J., Arkin I.T., and Dupree
P., 2002, Prediction of glycosylphosphatidylinositol-anchored
proteins in Arabidopsis. A genomic analysis, Plant
Physiol., 129: 486-499
http://dx.doi.org/10.1104/pp.010884
Boudart G., Minic Z., Albenne C., Canut H., Jamet E., and
Pont-Lezica R., 2007, Cell wall proteome, In: Samaj S.,
and Thelen J. (eds.), Plant Proteomics, Springer,
pp.169-185
Bouws H., Wattenberg A., and Zorn H., 2008, Fungal
secretomes-nature's toolbox for white biotechnology, Appl.
Microbiol. Biotechnol., 80: 381-388
http://dx.doi.org/10.1007/s00253-008-1572-5
Caccia D., Dugo M., Callari M., and Bongarzone I., 2013,
Bioinformatics tools for secretome analysis, Biochim.
Biophys. Acta., S1570-9639
Chen X.Y., Kim S.T., Cho W.K., Rim Y., Kim S., Kim S.W.,
Kang K.Y., Park Z.Y., and Kim J.Y., 2009, Proteomics of
weakly bound cell wall proteins in rice calli, J. Plant
Physiol., 166: 675-685
http://dx.doi.org/10.1016/j.jplph.2008.09.010
Cheng F.Y., and Williamson J.D., 2010, Is there leaderless
protein secretion in plants? Plant Signal Behav., 5:
129-131
http://dx.doi.org/10.4161/psb.5.2.10304
Cho W.K., and Kim J.Y., 2009, Integrated analyses of the rice
secretome, Plant Signal Behav., 4: 345-347
http://dx.doi.org/10.4161/psb.4.4.8198
Cho W.K., Chen X.Y., Chu H., Rim Y., Kim S., Kim S.T., Kim
S.W., Park Z.Y., and Kim J.Y., 2009, Proteomic analysis
of the secretome of rice calli, Physiol. Plant, 135: 331-341
http://dx.doi.org/10.1111/j.1399-3054.2008.01198.x
Chou K.C., and Shen H.B., 2008, Cell-PLoc: a package of Web
servers for predicting subcellular localization of proteins
in various organisms, Nat. protoc., 3(2): 153-162
http://dx.doi.org/10.1038/nprot.2007.494
de Castro E., Sigrist C.J., Gattiker A., Bulliard V.,
Langendijk-Genevaux P.S., Gasteiger E., Bairoch A., and
Hulo N., 2006, ScanProsite: detection of PROSITE
signature matches and ProRule-associated functional and
structural residues in proteins, Nucleic Acids Res.,
34(Web Server issue): W362-365
De-la-Peña C., Badri D.V., Lei Z., Watson B.S., Brandão M.M.,
Silva-Filho M.C., Sumner L.W., and Vivanco J.M., 2010,
Root
secretion of defense-related proteins is
development-dependent and correlated with flowering
time, J. Biol. Chem., 285: 30654-30665
http://dx.doi.org/10.1074/jbc.M110.119040
Ding Y., Wang J., Wang J., Stierhof Y.D., Robinson D.G., and
Jiang L., 2012, Unconventional protein secretion, Trends
Plant Sci., 7: 606-615
http://dx.doi.org/10.1016/j.tplants.2012.06.004
Duvick J., Fu A., Muppirala U., Sabharwal M., Wilkerson M.D.,
Lawrence C.J., Lushbough C., and Brendel V., 2008,
Computational
Molecular Biology