Computational identification and systematic classification of novel GRAS genes in Isatis indigotica

Chinese Journal of Natural Medicines - Tập 14 - Trang 161-176 - 2016
Lei ZHANG1,2, Qing LI1, Jun-Feng CHEN1, Wan-Sheng CHEN1
1Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
2Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China

Tài liệu tham khảo

Sun, 1996, Redox regulation of transcriptional activators [J], Free Radic Biol Med, 21, 335, 10.1016/0891-5849(96)00109-8

Zhang, 2014, Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza [J], J Integr Plant Biol, 56, 38, 10.1111/jipb.12111

Pysh, 1999, The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW–LIKE genes [J], Plant J, 18, 111, 10.1046/j.1365-313X.1999.00431.x

Peng, 1997, The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses [J], Genes Dev, 11, 3194, 10.1101/gad.11.23.3194

Silverstone, 1998, The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway [J], Plant Cell, 10, 155, 10.1105/tpc.10.2.155

Bolle, 2000, PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction [J], Genes Dev, 14, 1269, 10.1101/gad.14.10.1269

Greb, 2003, Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation [J], Genes Dev, 17, 1175, 10.1101/gad.260703

Stuurman, 2002, Shoot meristem maintenance is controlled by a GRAS-gene mediated signal from differentiating cells [J], Genes Dev, 16, 2213, 10.1101/gad.230702

Di Laurenzio, 1996, The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root [J], Cell, 86, 423, 10.1016/S0092-8674(00)80115-4

Helariutta, 2000, The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling [J], Cell, 101, 555, 10.1016/S0092-8674(00)80865-X

Morohashi, 2003, Isolation and characterization of a novel GRAS gene that regulates meiosis-associated gene expression [J], J Biol Chem, 278, 20865, 10.1074/jbc.M301712200

Czikkel, 2007, NtGRAS1, a novel stress-induced member of the GRAS family in tobacco, localizes to the nucleus [J], J Plant Physiol, 164, 1220, 10.1016/j.jplph.2006.07.010

Song, 2014, Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis) [J], Genomics, 103, 135, 10.1016/j.ygeno.2013.12.004

Chinese Pharmacopoeia Commission, 2010, 191

Chen, 2013, Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling [J], BMC genomics, 14, 857, 10.1186/1471-2164-14-857

Guo, 2005, DATF: a database of Arabidopsis transcription factors [J], Bioinformatics, 21, 2568, 10.1093/bioinformatics/bti334

Punta, 2012, The Pfam protein families database [J], Nucleic Acids Res, 40, D290, 10.1093/nar/gkr1065

Letunic, 2012, SMART 7: recent updates to the protein domain annotation resource [J], Nucleic Acids Res, 40, D302, 10.1093/nar/gkr931

Gasteiger, 2005, 571

Combet, 2000, NPS@: network protein sequence analysis [J], Trends Biochem Sci, 25, 147, 10.1016/S0968-0004(99)01540-6

Llave, 2002, Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA [J], Science, 297, 2053, 10.1126/science.1076311

Xue, 2010, PONDR-FIT: a meta-predictor of intrinsically disordered amino acids [J], Biochim Biophys Acta, 1804, 996, 10.1016/j.bbapap.2010.01.011

Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools [J], Nucleic Acids Res, 25, 4876, 10.1093/nar/25.24.4876

Bailey, 2009, MEME SUITE: tools for motif discovery and searching [J], Nucleic Acids Res, 37, W202, 10.1093/nar/gkp335

Franceschini, 2013, STRING v9. 1: protein-protein interaction networks, with increased coverage and integration [J], Nucleic Acids Res, 41, D808, 10.1093/nar/gks1094

Saeed, 2003, TM4: a free, open-source system for microarray data management and analysis [J], Biotechniques, 34, 374, 10.2144/03342mt01

Lee, 2008, Large-scale analysis of the GRAS gene family in Arabidopsis thaliana [J], Plant Mol Biol, 67, 659, 10.1007/s11103-008-9345-1

Miyashima, 2009, ARGONAUTE1 acts in Arabidopsis root radial pattern formation independently of the SHR/SCR pathway [J], Plant Cell Physiol, 50, 626, 10.1093/pcp/pcp020

Lee, 2002, Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibitions [J], Genes Dev, 16, 646, 10.1101/gad.969002

Wen, 2002, Arabidopsis RGL1 encodes a negative regulator of gibberellin responses [J], Plant Cell, 14, 87, 10.1105/tpc.010325

Dill, 2001, The DELLA motif is essential for gibberellin-induced degradation of RGA [J], Proc Natl Acad Sci USA, 98, 14162, 10.1073/pnas.251534098

Piskurewicz, 2009, The GA-signaling repressor RGL3 represses testa rupture in response to changes in GA and ABA levels [J], Plant Signal Behav, 4, 63, 10.4161/psb.4.1.7331

Ambros, 2004, The functions of animal microRNAs [J], Nature, 431, 350, 10.1038/nature02871

Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function [J], Cell, 116, 281, 10.1016/S0092-8674(04)00045-5

Torres-Galea, 2013, Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction [J], Plant Physiol, 161, 291, 10.1104/pp.112.206607

Li, 2003, Control of tillering in rice [J], Nature, 422, 618, 10.1038/nature01518

Dhondt, 2010, SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis by stimulating S-phase progression of the cell cycle [J], Plant Physiol, 154, 1183, 10.1104/pp.110.158857

Sozzani, 2010, Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth [J], Nature, 466, 128, 10.1038/nature09143

Wang, 2011, The genome of the mesopolyploid crop species Brassica rapa [J], Nat Genet, 43, 1035, 10.1038/ng.919

Hirano, 2010, Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice [J], Plant Cell, 22, 2680, 10.1105/tpc.110.075549

Koizumi, 2013, Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning [J], Development, 140, 1292, 10.1242/dev.090761

Gao, 2004, An auxin-responsive SCARECROW-like transcriptional activator interacts with histone deacetylase [J], Plant Mol Biol, 55, 417, 10.1007/s11103-004-0892-9

Welch, 2007, Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action [J], Genes Dev, 21, 2196, 10.1101/gad.440307