دورية أكاديمية
Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.
العنوان: | Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. |
---|---|
المؤلفون: | Ghorbani S; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Lin YC; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Parizot B; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Fernandez A; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Njo MF; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Van de Peer Y; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa., Beeckman T; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium., Hilson P; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences, INRA, route de Saint-Cyr, 78026 Versailles, France pierre.hilson@versailles.inra.fr. |
المصدر: | Journal of experimental botany [J Exp Bot] 2015 Aug; Vol. 66 (17), pp. 5257-69. Date of Electronic Publication: 2015 Jul 20. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9882906 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1460-2431 (Electronic) Linking ISSN: 00220957 NLM ISO Abbreviation: J Exp Bot Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Oxford, UK : Oxford University Press, |
مواضيع طبية MeSH: | Genome, Plant*, Genomics/*methods , Peptides/*genetics , Plant Development/*genetics , Plant Proteins/*genetics, Conserved Sequence ; Gene Expression Profiling ; Microsatellite Repeats ; Peptides/metabolism ; Phylogeny ; Plant Proteins/metabolism ; Plant Roots/genetics ; Plant Roots/growth & development |
مستخلص: | Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes. (© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.) |
References: | Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5235-40. (PMID: 23479623) Dev Cell. 2012 Mar 13;22(3):678-85. (PMID: 22421050) BMC Bioinformatics. 2004 Aug 19;5:113. (PMID: 15318951) Nucleic Acids Res. 2008 Jan;36(Database issue):D1028-33. (PMID: 18089549) Nucleic Acids Res. 2002 Apr 1;30(7):1575-84. (PMID: 11917018) Stat Appl Genet Mol Biol. 2004;3:Article3. (PMID: 16646809) Plant Cell. 2012 Aug;24(8):3198-217. (PMID: 22932676) Methods Mol Biol. 2010;615:375-83. (PMID: 20013221) Nature. 2007 Sep 27;449(7161):463-7. (PMID: 17721507) Plant Cell. 2002 Oct;14(10):2339-51. (PMID: 12368490) Plant Signal Behav. 2014;9(2):e27848. (PMID: 24526015) J Exp Bot. 2015 Aug;66(17):5351-65. (PMID: 26062745) Science. 2010 Aug 27;329(5995):1065-7. (PMID: 20798316) Bioinformatics. 2008 Nov 15;24(22):2630-1. (PMID: 18845584) Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2395-400. (PMID: 23341627) PLoS Pathog. 2014 Sep 04;10(9):e1004331. (PMID: 25188390) Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1479-88. (PMID: 22527390) Trends Plant Sci. 2009 May;14(5):255-63. (PMID: 19362511) Plant Physiol. 2010 May;153(1):34-40. (PMID: 20219832) Nat Protoc. 2007;2(4):953-71. (PMID: 17446895) Science. 2009 Nov 20;326(5956):1112-5. (PMID: 19965430) Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7. (PMID: 17145706) Science. 2007 Nov 2;318(5851):801-6. (PMID: 17975066) Methods Mol Biol. 2000;132:185-219. (PMID: 10547837) Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18333-8. (PMID: 17989228) Development. 1997 Jan;124(1):33-44. (PMID: 9006065) Biostatistics. 2003 Apr;4(2):249-64. (PMID: 12925520) J Exp Bot. 2013 Dec;64(17):5395-409. (PMID: 24259455) Plant Cell Physiol. 2013 Mar;54(3):369-74. (PMID: 23256149) BMC Plant Biol. 2008 Jan 03;8:1. (PMID: 18171480) Dev Cell. 2013 Jul 29;26(2):136-47. (PMID: 23850190) J Mol Biol. 2004 Jul 16;340(4):783-95. (PMID: 15223320) Science. 2008 Oct 24;322(5901):594-7. (PMID: 18948541) Plant Cell Physiol. 2007 Mar;48(3):471-83. (PMID: 17284469) Plant Physiol. 2014 Oct;166(2):538-50. (PMID: 25136060) Mol Cell Proteomics. 2013 May;12(5):1158-69. (PMID: 23328941) Biotechniques. 2003 Feb;34(2):374-8. (PMID: 12613259) Plant Cell. 2011 Oct;23(10):3671-83. (PMID: 22003076) Science. 2013 Nov 15;342(6160):860-3. (PMID: 24158907) Plant Cell Physiol. 2012 Dec;53(12):1989-99. (PMID: 23045524) Plant Cell. 2013 Jul;25(7):2444-63. (PMID: 23903317) Annu Rev Plant Biol. 2014;65:385-413. (PMID: 24779997) Plant J. 2009 Sep;59(6):930-9. (PMID: 19473327) Front Plant Sci. 2013 Sep 06;4:352. (PMID: 24046775) J Exp Bot. 2013 Dec;64(17):5371-81. (PMID: 24179095) Plant J. 2008 Jul;55(1):152-60. (PMID: 18315543) J Exp Bot. 2013 Dec;64(17):5383-94. (PMID: 24179096) Rice (N Y). 2013 Feb 06;6(1):4. (PMID: 24280374) Plant J. 2007 Jul;51(2):262-80. (PMID: 17565583) Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):15067-72. (PMID: 19666544) Nat Chem Biol. 2012 Sep;8(9):798-805. (PMID: 22885787) Science. 2010 Sep 10;329(5997):1306-11. (PMID: 20829477) Commun Integr Biol. 2013 Nov 1;6(6):e26531. (PMID: 24563707) Plant Physiol. 2006 Aug;141(4):1284-92. (PMID: 16751438) Science. 2006 Sep 15;313(5793):1596-604. (PMID: 16973872) Chembiochem. 2000 Nov 17;1(4):214-46. (PMID: 11828414) Plant Mol Biol. 2009 Mar;69(4):383-96. (PMID: 18807199) PLoS Biol. 2006 May;4(5):e143. (PMID: 16640459) Plant Cell. 2005 Nov;17(11):3035-50. (PMID: 16243906) Curr Opin Plant Biol. 2015 Feb;23:8-14. (PMID: 25449721) Curr Biol. 2009 Jun 9;19(11):909-14. (PMID: 19398337) Curr Biol. 2010 Oct 12;20(19):1697-706. (PMID: 20888232) Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1760-5. (PMID: 22307643) Plant Physiol. 2013 Feb;161(2):954-70. (PMID: 23370719) Bioinformatics. 2005 Jun 15;21(12):2912-3. (PMID: 15827079) |
فهرسة مساهمة: | Keywords: Crops; genome annotation; meta-analysis; plant development; signalling peptide. |
المشرفين على المادة: | 0 (Peptides) 0 (Plant Proteins) |
تواريخ الأحداث: | Date Created: 20150722 Date Completed: 20160524 Latest Revision: 20240518 |
رمز التحديث: | 20240518 |
مُعرف محوري في PubMed: | PMC4526923 |
DOI: | 10.1093/jxb/erv346 |
PMID: | 26195730 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1460-2431 |
---|---|
DOI: | 10.1093/jxb/erv346 |