LIM Family from Maize

Required domains for LIM family:PF00412

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In animals, genes of the LIM homeobox (Lhx) family perform fundamental roles in tissue-specific differentiation and body patterning during development in both vertebrates and invertebrates. These genes comprise a family of DNA-binding proteins with six subfamilies; each subfamily member is represented once in Caenorhabditis elegans and Drosophila melanogaster and twice in mammalian species (Hobert et al., 2000). Lhx proteins include two N-terminal LIM domains (named after the founding members LIN-11, Islet-1, and MEC-3) which are now recognized as tandem cysteine rich, zinc-finger structures that function as a modular protein-binding interface.  Secondly they include a helix-turn-helix forming homeodomain that binds regulatory DNA surrounding target genes (Kadrmas et al., 2004, Gehring et al., 1994, Srivastava et al., 2010). The zinc-finger forming LIM domains are essential for protein function in several subfamilies and are thought to regulate DNA binding by the homeodomain by interacting with other nuclear proteins (Srivastava et al., 2010). LIM proteins are thought to function as biosensors that mediate communication between the cytosolic and the nuclear compartments (Kadrmas et al., 2004).  LIM domain containing genes have been identified in plants but they do not harbor the homeodomin that is present in animal Lhx genes. It remains unclear which domain may interact with DNA in plant LIMs.

In plants, HaP-LIM1 was first isolated from sunflower (Helianthus annuus L.) pollen, and then in tobacco (Nicotiana tabacum L.), and later in Arabidopsis (Papuga et al., 2010). The LIM genes in plants are comprised of two sub-families based on the number of LIM domains: single LIM sub-family (DA1/DAR) and double LIM sub-family (2LIMs) (Nian et al., 2021). The 2LIM protein contains two LIM domains (PF00412) separated by 40–50 amino acid residues [(C-X2-C-X17-H-X2-C)-X2-(C-X2-C-X17-C-X2-H) and (C-X2-C-X17-H-X2-C)-X2-(C-X4-C-X15-C-X2-H). Structurally, the 2LIM subfamily in the plant is similar to the domains of cysteine-rich protein (CRP) family members in animals, but there are some differences. The plant 2LIM protein contains a variable short C-terminus and lacks a Glycine region. Based on their expression mode, 2LIM proteins are divided into two types: WLIM (WLIM1 and WLIM2), which is widely expressed in various tissues, and PLIM (PLIM1 and PLIM2), which is widely expressed in pollen tubes (Eliasson et al., 2000). The DA1 & DAR sub-family is present only in plants and contains a conserved LIM domain and a domain of unknown function (PF12315) (Zhao et al., 2014). According to the amino acid sequence, DA1 & DAR proteins are divided into two types: Class I and Class II. So far, DA1 & DAR LIM proteins have been identified only in land plants. The subcellular localization of plant LIM proteins is the same as that of animals, with three simultaneous localizations of cytoplasm, nucleus, and nucleoplasm (Nian et al., 2021). Nuclear LIM domain proteins are thought to function as TFs involved in tissue specific gene regulation and cell fate determination, whereas, cytoplasmic LIM domain proteins are known to actively participate in cytoskeleton organization through regulation of actin dynamics. However, dual functioning has also been well documented. In tobacco (N. tabacum), NtLIM2 protein exhibited a twin role through actin-bundling and histone gene transcription (Moes et al., 2013). Similarly, in cotton (G. hirsutum), GhWLIM1a and GhXLIM6 proteins showed altered fiber properties including fiber length, fineness and strength via modulating both F-actin dynamics and transcription of genes involved in phenyl-propanoid pathway (Han et al., 2013).

There is some evidence that the tobacco NtWLIM1 protein can activate key enzymes in the phenylpropanoid metabolic pathway in a PAL-box dependent manner and thus participate in the regulation of lignin biosynthesis. Transgenic tobacco plants with antisense Ntlim1 showed low levels of transcripts from some key phenylpropanoid pathway genes such as phenylalanine ammonia-lyase, hydroxycinnamate CoA ligase and cinnamyl alcohol dehydrogenase. Furthermore, a 27% reduction of lignin content was observed in the transgenic tobacco with antisense Ntlim1 (Kawaoka et al., 2000). In maize, transcriptomic and metabolic profiling revealed a lignin metabolism network involved in mesocotyl elongation during maize seed germination that implicated MYB, NAC, WRKY, and LIM TF family members (Zhao et al., 2022).

Last updated June 2023 by John Gray


Srivastava M, Larroux C, Lu DR, Mohanty K, Chapman J, Degnan BM, Rokhsar DS. Early evolution of the LIM homeobox gene family. BMC Biol. 2010 Jan 18;8:4. doi: 10.1186/1741-7007-8-4. PMID: 20082688; PMCID: PMC2828406.

Papuga J, Hoffmann C, Dieterle M, Moes D, Moreau F, Tholl S, Steinmetz A, Thomas C. Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation. Plant Cell. 2010 Sep;22(9):3034-52. doi: 10.1105/tpc.110.075960. Epub 2010 Sep 3. PMID: 20817848; PMCID: PMC2965535.

Hobert O, Westphal H. Functions of LIM-homeobox genes. Trends Genet. 2000 Feb;16(2):75-83. doi: 10.1016/s0168-9525(99)01883-1. PMID: 10652534.

Kadrmas JL, Beckerle MC. The LIM domain: from the cytoskeleton to the nucleus. Nat Rev Mol Cell Biol. 2004 Nov;5(11):920-31. doi: 10.1038/nrm1499. PMID: 15520811.

Gehring WJ, Affolter M, Bürglin T. Homeodomain proteins. Annu Rev Biochem. 1994;63:487-526. doi: 10.1146/ PMID: 7979246.

Nian L, Liu X, Yang Y, Zhu X, Yi X, Haider FU. Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L. PLoS One. 2021 Jun 30;16(6):e0252213. doi: 10.1371/journal.pone.0252213. PMID: 34191816; PMCID: PMC8244919.

Eliasson A, Gass N, Mundel C, Baltz R, Kräuter R, Evrard JL, Steinmetz A. Molecular and expression analysis of a LIM protein gene family from flowering plants. Mol Gen Genet. 2000 Oct;264(3):257-67. doi: 10.1007/s004380000312. PMID: 11085265.

Zhao M, He L, Gu Y, Wang Y, Chen Q, He C. Genome-wide analyses of a plant-specific LIM-domain gene family implicate its evolutionary role in plant diversification. Genome Biol Evol. 2014 Apr;6(4):1000-12. doi: 10.1093/gbe/evu076. PMID: 24723730; PMCID: PMC4007552.

Kawaoka A, Kaothien P, Yoshida K, Endo S, Yamada K, Ebinuma H. Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. Plant J. 2000 May;22(4):289-301. doi: 10.1046/j.1365-313x.2000.00737.x. PMID: 10849346.

Zhao X, Niu Y, Bai X, Mao T. Transcriptomic and Metabolic Profiling Reveals a Lignin Metabolism Network Involved in Mesocotyl Elongation during Maize Seed Germination. Plants (Basel). 2022 Apr 11;11(8):1034. doi: 10.3390/plants11081034. PMID: 35448762; PMCID: PMC9027596.

Moes D, Gatti S, Hoffmann C, Dieterle M, Moreau F, Neumann K, Schumacher M, Diederich M, Grill E, Shen WH, Steinmetz A, Thomas C. A LIM domain protein from tobacco involved in actin-bundling and histone gene transcription. Mol Plant. 2013 Mar;6(2):483-502. doi: 10.1093/mp/sss075. Epub 2012 Aug 28. PMID: 22930731; PMCID: PMC3603003.

Han LB, Li YB, Wang HY, Wu XM, Li CL, Luo M, Wu SJ, Kong ZS, Pei Y, Jiao GL, Xia GX. The dual functions of WLIM1a in cell elongation and secondary wall formation in developing cotton fibers. Plant Cell. 2013 Nov;25(11):4421-38. doi: 10.1105/tpc.113.116970. Epub 2013 Nov 12. PMID: 24220634; PMCID: PMC3875727.




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