TCP Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for TCP family:PF03634

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The TCP family of transcription factors were named after the first four characterized members, including teosinte branched1 (TB1, ZmTCP1) from maize (Zea mays), cycloidea (CYC) from snapdragon (Antirrhinum majus) and proliferating cell factors 1 and 2 (PCF1 and PCF2) from rice (Oryza sativa) (Luo et al., 1996, Kosugi and Ohashi 1997, Cubas et al., 1999). TCP genes encode structurally related proteins that are implicated in the evolution of key morphological traits (Li, 2015).

TCP proteins are characterized by a highly conserved, approximately 60 residue TCP domain in the N-terminal region, which contains a basic helix-loop-helix (bHLH) structure involved in DNA binding and protein interactions (Cubas et al., 1999, Li, 2015). TCP proteins have been divided into two main classes, I (or PCF) and II (or CYC/TB1) (Viola et al., 2023). Class II TCPs are further divided into two clades: CYC/TB1 (or ECE) and CIN (CINCINNATA-like). The difference between both classes lies in features located both within and outside the TCP domain. Within the TCP domain, each subfamily differs in the length of the basic region, the composition of their bipartite nuclear localization signal (NLS), the residue composition of the loop and hydrophilic faces of the helices, and the length of helix II. Outside the TCP domain, class I TCPs have short regions flanking the domain while most of the class II TCPs have an arginine-rich domain or R domain and an ECE motif (glutamic acid-cysteine-glutamic acid) between the TCP and R domains (Viola et al., 2023). Class I TCP proteins recognize the consensus binding sequence GGNCCCAC, whereas class II proteins prefer the rather similar sequence GGGNCCAC and the different specificity of both classes has been attributed to changes in the identity of a specific residue located in the basic region (Viola et al., 2012).

The initial members of the TCP family were implicated in affecting cell division and morphological traits. SInce then TCPs have been shown to regulate plant development and the fine tuning of defense responses via stimulating the biosynthetic pathways of bioactive metabolites, such as brassinosteroid (BR), jasmonic acid (JA) and flavonoids (Li, 2015). In Arabidopsis, experiments indicate that AtTCP3 interactions with R2R3-MYBs lead to enhanced flavonoid production (Li et al., 2013).

In the maize genome, 29 TCP genes have been identified and they are unevenly distributed on the 10 maize chromosomes. These genes were categorized into nine classes based on phylogeny and purifying selection may largely be responsible for maintaining the functions of maize TCP genes (Chai et al., 2017). Expression analysis revealed that most maize TCP genes are expressed in the stem and ear, which suggests that ZmTCP genes influence stem and ear growth. This result is consistent with the previous finding that maize TCP genes represses the growth of axillary organs and enables the formation of female inflorescences (Chai et al., 2017). The first TCP gene to be cloned in maize was TB1 (ZmTCP1) which had previously been linked to increased apical dominance in domesticated maize. The pattern of tb1 expression and the morphology of tb1 mutant plants suggest that tb1 acts both to repress the growth of axillary organs and to enable the formation of female inflorescences. The maize allele of tb1 is expressed at twice the level of the teosinte allele, suggesting that gene regulatory changes underlie the evolutionary divergence of maize from teosinte. (Doebley et al., 1997, Prakash et al., 2020).

Last updated June 2023 by John Gray


Luo D, Carpenter R, Vincent C, Copsey L, Coen E. Origin of floral asymmetry in Antirrhinum. Nature. 1996 Oct 31;383(6603):794-9. doi: 10.1038/383794a0. PMID: 8893002.

Chai W, Jiang P, Huang G, Jiang H, Li X. Identification and expression profiling analysis of TCP family genes involved in growth and development in maize. Physiol Mol Biol Plants. 2017 Oct;23(4):779-791. doi: 10.1007/s12298-017-0476-1. Epub 2017 Oct 11. PMID: 29158628; PMCID: PMC5671458.

Kosugi S, Ohashi Y. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell. 1997 Sep;9(9):1607-19. doi: 10.1105/tpc.9.9.1607. PMID: 9338963; PMCID: PMC157037.

Li S. The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development. Plant Signal Behav. 2015;10(7):e1044192. doi: 10.1080/15592324.2015.1044192. PMID: 26039357; PMCID: PMC4622585.

Cubas P, Lauter N, Doebley J, Coen E. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 1999 Apr;18(2):215-22. doi: 10.1046/j.1365-313x.1999.00444.x. PMID: 10363373.

Viola IL, Alem AL, Jure RM, Gonzalez DH. Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors. Int J Mol Sci. 2023 Mar 12;24(6):5437. doi: 10.3390/ijms24065437. PMID: 36982512; PMCID: PMC10049435.

Viola IL, Reinheimer R, Ripoll R, Manassero NGU, Gonzalez DH. Determinants of the DNA binding specificity of class I and class II TCP transcription factors. J Biol Chem. 2012 Jan 2;287(1):347-356. doi: 10.1074/jbc.M111.256271. Epub 2011 Nov 10. PMID: 22074922; PMCID: PMC3249086.

Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature. 1997 Apr 3;386(6624):485-8. doi: 10.1038/386485a0. PMID: 9087405.

Prakash NR, Chhabra R, Zunjare RU, Muthusamy V, Hossain F. Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives. 3 Biotech. 2020 Feb;10(2):77. doi: 10.1007/s13205-020-2052-6. Epub 2020 Jan 29. PMID: 32058540; PMCID: PMC6987282.

Li S, Zachgo S. TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana. Plant J. 2013 Dec;76(6):901-13. doi: 10.1111/tpj.12348. Epub 2013 Nov 12. PMID: 24118612.




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