Homeobox Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for Homeobox family:PF00046

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Genetic analysis of plant architecture has led to the discovery of key genes that function in meristems, including the maize (Zea mays) transcription factor knotted1 (kn1), the founding member of the kn1 homeobox (knox) gene family (Vollbrecht et al., 1991, Bolduc et al., 2014). The Knotted-1 (Kn1) locus was first defined by several dominant gain-of-function mutations that altered leaf development. Foci of cells along the lateral veins do not differentiate properly, but continue to divide, forming outpocketings or “knots” (Vollbrecht et al., 1991). The maize Kn1 gene was found to encode a homeodomain-containing protein, the first identified in the plant kingdom. Genes containing the homeobox domain were discovered for the first time in Drosophila. This was due to the homeotic mutation, which transformed one part into another part in the Drosophila body. Homeobox domain genes are mainly involved in controlling the growth and developmental processes such as transition through phases in an organism by encoding a certain transcription factor. The presence of a homeodomain (HD), which comprises 60 amino acids, makes a three-helix tertiary structure, that binds the promoter regions of specific target genes (Sharif et al., 2021).

Since the discovery of the Kn1 gene, a large number of transcription factor (TF) genes encoding proteins with homeodomains have been found in all plants and there are about 135 family members in maize. Many of these contain additional domains that define subfamilies.

The zinc finger-homeodomain (ZF-HD) TFs, containing a conserved zinc finger (ZF) domain in the N-terminal and a homeodomain (HD) in the C-terminal. In maize a total of 21 ZHD genes with different physicochemical properties were found distributed on nine chromosomes in maize (Islam et al., 2022).

The HD-ZIP gene family is composed of two functional domains, i.e., HD and a leucine zipper (LZ). Based on their sequence conservation and functional properties, HD-ZIP can be further divided into four subfamilies (HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV) (Sharif et al., 2021). ZmHOX32, a member of the HD-ZIP III family (that also harbor a START domain that is able to bind to steroid ligands), appears to function in leaf morphogenesis and plant photosynthesis as judged by the enriched category of downstream genes that it regulates (Miao et al., 2023). In Arabidopsis, Hox32 homologs IFL1, ATHB-9 and ATHB-14 are involved in the development of the apical meristem, vascular bundle and the paraxial region of the lateral tissue, regulating the embryonic development process in the formation of the root tip

Loss-of-function mutants highlight the requirement for knox genes in shoot function. The first discovered knox loss-of-function mutant, shoot meristemless (stm) of Arabidopsis (Arabidopsis thaliana), fails to produce shoot organs after the cotyledons have formed (Long et al., 1996).

Last updated June 2023 by John Gray


Vollbrecht E, Veit B, Sinha N, Hake S. The developmental gene Knotted-1 is a member of a maize homeobox gene family. Nature. 1991 Mar 21;350(6315):241-3. doi: 10.1038/350241a0. PMID: 1672445.

Bolduc N, Tyers RG, Freeling M, Hake S. Unequal redundancy in maize knotted1 homeobox genes. Plant Physiol. 2014 Jan;164(1):229-38. doi: 10.1104/pp.113.228791. Epub 2013 Nov 11. PMID: 24218490; PMCID: PMC3875803.

Sharif R, Raza A, Chen P, Li Y, El-Ballat EM, Rauf A, Hano C, El-Esawi MA. HD-ZIP Gene Family: Potential Roles in Improving Plant Growth and Regulating Stress-Responsive Mechanisms in Plants. Genes (Basel). 2021 Aug 17;12(8):1256. doi: 10.3390/genes12081256. PMID: 34440430; PMCID: PMC8394574.

Long JA, Moan EI, Medford JI, Barton MK. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature. 1996 Jan 4;379(6560):66-9. doi: 10.1038/379066a0. PMID: 8538741.

Islam MAU, Nupur JA, Khalid MHB, Din AMU, Shafiq M, Alshegaihi RM, Ali Q, Ali Q, Kamran Z, Manzoor M, Haider MS, Shahid MA, Manghwar H. Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L. Genes (Basel). 2022 Nov 14;13(11):2112. doi: 10.3390/genes13112112. PMID: 36421787; PMCID: PMC9690586.

Miao X, Zhu W, Jin Q, Song Z, Li L. ZmHOX32 is related to photosynthesis and likely functions in plant architecture of maize. Front Plant Sci. 2023 Mar 22;14:1119678. doi: 10.3389/fpls.2023.1119678. PMID: 37035059; PMCID: PMC10073575.





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