Sequence analysis of Squamosa promoter binding protein (SBP) transcription factors
The Squamosa promoter binding proteins (SBPs) are a family of plant-specific transcription factors.
They play critical roles in regulating flower and fruit development as well as other physiological processes.
SBP-box genes encode proteins sharing a conserved DNA-binding domain of 79 amino acid residues. the DNA-binding
domain of SBPs consisted of two separate zinc-binding sites. One zinc finger is C3H or C4 and the other is C2HC.
Guo et al (2008) made a genome-wide identification of SBP-box genes from 9 species representing the main plant lineages and
performed phylogenetic analysis and classification to explore the evolution of SBP-box gene family. We use the SBP TF family
as a example to study tools for the analysis of the exon-intron structure, the pattern of the conserved motifs,
and the construction of phylogenetics tree.
Exercises
-
Find protein sequences of all Arabidopsis squamosa promoter binding
transcription factors (SBP) from the database of Arabidopsis transcription
factors
(DATF).
-
Make sequence alignment of SPL3 and SPL4. Find exons from these two SBP TFs
using the
GSDS
online web server.
-
Find functional domains of SPL1 and SPL3 using SMART.
-
Find conserved domains for among 15 Arabidopsis SBP TFs
(15ATSBP.FAS).
-
Make phylogenetic analysis for Arabidopsis 15 SBP DNA binding domains
(15ATSBPD.FAS)
-
Build HMM model for 15 SBP DNA binding domains
(15ATSBPD.FAS).
-
Search sequence database for the multiple sequence alignment of 15 SBP DNA binding domains
(15ATSBPD.aln).
-
Search SBP DNA binding domains against maize transcription factors using the
above HMM model.
-
Compare the above BLAST and HMM search results.
-
Find all putative SBP genes via BLAST search against all online genome
databases.
-
Make local Blast search against a set of maize TFs using the SPL3 protein and
CDS sequences.
(ZMTF_CDS.FAS).
Data
-
17AT_SPL.FAS
- The protein sequence of 17 Arabidopsis transcription factors from the SBP
family.
-
19OJ_SPL.FAS
- The protein sequence of 17 Arabidopsis transcription factors from the SBP
family.
-
35ATSPL7H.FAS
- The protein sequence of 35 homologus of SPL7_ARATH
retrieved and modified
from
OMA
-
15ATSBP.FAS
- The protein sequence of 15 Arabidopsis transcription factors from the SBP
family.
-
15ATSBPD.FAS
- The protein sequence of the DNA-binding domain of 15 Arabidopsis
transcription factors from the SBP family.
-
15ATSBPD.ALN
- The ClustalW output of the DNA-binding domain of 15 Arabidopsis
transcription factors from the SBP family.
-
ZMTF_CDS.FAS
- The coding sequence of 764 maize (Zea mays) transcription factors.
-
ZMTF_PEP.FAS
- The protein sequence of 764 maize (Zea mays) transcription factors.
-
SPL3_CDS.FAS
- The coding sequence of the Arabidopsis transcription factor SPL3.
-
SPL3_PEP.FAS
- The protein sequence of the Arabidopsis transcription factor SPL3.
References
-
Luo JC, Analysis of Arabidopsis SBP gene family (in Chinese).
[PDF]
-
Guo AY, Zhu QH, Gu XC, Ge S, Yan J and Luo JC.
Genome-wide identification and evolutionary analysis of the plant specific
SBP-box transcription factor family. Gene. 2008 Jul 15;418(1-2):1-8.
[Abstract]
[PDF]
-
Yang Z, Wang X, Gu S, Hu Z, Xu H, Xu C.
Comparative study of SBP-box gene family in Arabidopsis and rice.
Gene. 2008 Jan 15;407(1-2):1-11.
[Abstarct]
[PDF]
-
Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, ..., Doebley JF.
The origin of the naked grains of maize.
Nature. 2005 Aug 4;436(7051):714-719.
[Abstract]
[PDF]
-
Manning K, Tor M, Poole M, Hong Y, Thompson AJ, ..., Seymour GB.
A naturally occurring epigenetic mutation in a gene encoding an SBP-box
transcription factor inhibits tomato fruit ripening.
Nat Genet. 2006 Aug;38(8):948-52.
[Abstract]
[PDF]
-
Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, ..., Li J.
Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.
Nat Genet. 2010 Jun;42(6):541-4.
[Abstract]
[PDF]
-
Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, ..., Ashikari M.
OsSPL14 promotes panicle branching and higher grain productivity in rice.
Nat Genet. 2010 Jun;42(6):545-9.
[Abstract]
[PDF]
-
Si L, Chen J, Huang X, Gong H, ..., Han B.
OsSPL13 controls grain size in cultivated rice.
Nat Genet. 2016 Apr;48(4):447-56. 2010 Jun;42(6):545-9.
[Abstract]
[PDF]
-
Yao, S., Yang, Z., Yang, R., Huang, Y., Guo, G., Kong, X., Li, Y. (2019).
Transcriptional Regulation of miR528 by OsSPL9 Orchestrates Antiviral
Response in Rice. Molecular plant, 12(8), 1114-22.
[Abstract]
[PDF]
[Supplemental]
-
Zhang, H., Zhao, X., Li, J., Cai, H., Deng, X. W., & Li, L. (2014).
MicroRNA408 is critical for the HY5-SPL7 gene network that mediates
the coordinated response to light and copper.
The Plant cell, 26(12), 4933-4953.
[Abstract]
-
Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P.
Molecular characterisation of the Arabidopsis SBP-box genes.
Gene. 1999 Sep 3;237(1):91-104.
[Abstract]
[PDF]
-
Riese M, Hohmann S, Saedler H, Münster T, Huijser P.
Comparative analysis of the SBP-box gene families in P. patens and seed
plants.
Gene. 2007;Oct 15;401(1-2):28-37.
[Abstract]
[PDF]