SBP Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for SBP family:PF03110

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The SPL (SQUAMOSA Promoter-Binding Protein-like (SPL) transcription factor gene family represents a group of structurally diverse genes encoding putative transcription factors found apparently only in plants. The distinguishing characteristic of the SPL gene family is the SBP-box encoding a conserved protein domain of 76 amino acids in length, the SBP-domain (PF03110) ((for SQUAMOSA-PROMOTER BINDING PROTEIN), which is responsible for the interaction with DNA (Cardon et al., 1999). The SBP domain consists of two separate zinc finger structures, which contain Zn-1(Cys3His or Cys4) and Zn-2(Cys2HisCys). The C-terminus of the SBP domain is rich in basic amino acids, which provide a bidirectional nuclear localization signal (NLS). The first members of this family were SBP1 and SBP2, isolated from Antirrhinum majus by their capacity to interact in vitro with a promoter sequence element of the floral meristem identity gene SQUAMOSA (Klein et al., 1996). As an important transcription factor, the SPL proteins activate or inhibit the expression of target genes by recognizing and binding to a GTAC element in the promoter regions of target genes.

In Arabidopsis there are 12 members in the SPL gene family which exhibit highly diverse genomic organizations. Some SPL genes are constitutively expressed, while transcriptional activity of others is under developmental control. Based on phylogenetic reconstruction, gene structure and expression patterns, they can be divided into subfamilies (Cardon et al., 1999).  AtSPL3 was reported to prevent early flowering in Arabidopsis (Gandikota et al., 2007), AtSPL9 and AtSPL15 controlled shoot maturation (Schwarz et al., 2008), and AtSPL9 regulated the vegetative phase change and cell elongation through the BR (brassinosteroid) signaling pathway (Wang et al., 2021). AtSPL8 has been identified as affecting GA (gibberellins) signaling (Zhang et al., 2007), while AtSPL9 negatively regulates anthocyanin accumulation through the destabilization of a MYB-bHLH-WD40 transcriptional activation complex (Guo et al., 2011).

At least 31 SPL family members have been identified in maize. Of these, 18 ZmSPL gene pairs (24 genes) were located on the segmental duplication regions, accounting for 77.4% of the number of ZmSPLs (Peng et al. 2019). ZmSPL4 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis the liguleless1 (lg1) gene (Moreno et al., 1997). The SBP-box transcription factor tasselsheath-4 (TSH4) was found to regulate bract development and the establishment of meristem boundaries in maize. TSH4 binds upstream of tasselsheath1 (tsh1) and the ligule identity gene liguleless2 (lg2) (Chuck et al., 2010, Xiao et al., 2022).

Last updated June 2023 by John Gray


Cardon G, Höhmann 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. doi: 10.1016/s0378-1119(99)00308-x. PMID: 10524240.

Klein J, Saedler H, Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol Gen Genet. 1996 Jan 15;250(1):7-16. doi: 10.1007/BF02191820. PMID: 8569690.

Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, Huijser P. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007 Feb;49(4):683-93. doi: 10.1111/j.1365-313X.2006.02983.x. Epub 2007 Jan 8. PMID: 17217458.

Schwarz S, Grande AV, Bujdoso N, Saedler H, Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol. 2008 May;67(1-2):183-95. doi: 10.1007/s11103-008-9310-z. Epub 2008 Feb 17. PMID: 18278578; PMCID: PMC2295252.

Wang L, Yu P, Lyu J, Hu Y, Han C, Bai MY, Fan M. BZR1 Physically Interacts with SPL9 to Regulate the Vegetative Phase Change and Cell Elongation in Arabidopsis. Int J Mol Sci. 2021 Sep 27;22(19):10415. doi: 10.3390/ijms221910415. PMID: 34638756; PMCID: PMC8509050.

Zhang Y, Schwarz S, Saedler H, Huijser P. SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol Biol. 2007 Feb;63(3):429-39. doi: 10.1007/s11103-006-9099-6. Epub 2006 Nov 9. PMID: 17093870.

Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011 Apr;23(4):1512-22. doi: 10.1105/tpc.111.084525. Epub 2011 Apr 12. PMID: 21487097; PMCID: PMC3101539.

Chuck G, Whipple C, Jackson D, Hake S. The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development. 2010 Apr;137(8):1243-50. doi: 10.1242/dev.048348. Epub 2010 Mar 10. Erratum in: Development. 2010 May;137(9):1585. PMID: 20223762.

Xiao Y, Guo J, Dong Z, Richardson A, Patterson E, Mangrum S, Bybee S, Bertolini E, Bartlett M, Chuck G, Eveland AL, Scanlon MJ, Whipple C. Boundary domain genes were recruited to suppress bract growth and promote branching in maize. Sci Adv. 2022 Jun 17;8(24):eabm6835. doi: 10.1126/sciadv.abm6835. Epub 2022 Jun 15. PMID: 35704576; PMCID: PMC9200273.

Peng X, Wang Q, Zhao Y, Li X, Ma Q. Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. Genet Mol Biol. 2019 Apr-Jun;42(2):380-394. doi: 10.1590/1678-4685-GMB-2017-0144. Epub 2019 Jul 1. PMID: 31271590; PMCID: PMC6726161.

Moreno MA, Harper LC, Krueger RW, Dellaporta SL, Freeling M. liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev. 1997 Mar 1;11(5):616-28. doi: 10.1101/gad.11.5.616. PMID: 9119226.



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