Abstract
The LIM (Lin-11, Isl-1 and Mec-3 domains) family is a key transcription factor widely distributed in animals and plants. The LIM proteins in plants are involved in the regulation of a variety of biological processes, including cytoskeletal organization, the development of secondary cell walls, and cell differentiation. It has been identified and analyzed in many species. However, the systematic identification and analysis of the LIM genes family have not yet been reported in alfalfa (Medicago sativa L.). Based on the genome-wide data of alfalfa, a total of 21 LIM genes were identified and named MsLIM01-MsLIM21. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the LIM gene family in alfalfa using bioinformatics methods. The results showed that these MsLIM genes were distributed unequally on 21 of the 32 chromosomes in alfalfa. Gene duplication analysis showed that segmental duplications were the major contributors to the expansion of the alfalfa LIM family. Based on phylogenetic analyses, the LIM gene family of alfalfa can be divided into four subfamilies: αLIM subfamily, βLIM subfamily, γLIM subfamily, and δLIM subfamily, and approximately all the LIM genes within the same subfamily shared similar gene structure. The 21 MsLIM genes of alfalfa contain 10 Motifs, of which Motif1 and Motif3 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of MsLIM genes. Real-time quantitative PCR demonstrated that MsLIM gene expression is induced by low temperature and salt. The present study serves as a basic foundation for future functional studies on the alfalfa LIM family.
Highlights
Transcription factors, known as trans-acting elements, regulate the expression of stressinducible genes by directly or indirectly binding the cis-elements in promoter regions
The size of the coding sequences (CDSs) of the members of the MsLIM gene family is between 433–1113 nucleotides
The amino acid lengths of the proteins encoded by these genes vary from 154aa to 212aa, the molecular weight ranges from 17.14kDa to 23.73 kDa, and the PI variation range of the encoded protein from 6.20–9.16, the GRAVY value of all MsLIM proteins is less than 0, indicating that these proteins are hydrophilic
Summary
Transcription factors, known as trans-acting elements, regulate the expression of stressinducible genes by directly or indirectly binding the cis-elements in promoter regions. The family of LIM proteins possesses a cysteine-rich zinc-binding domain named as LIM domain [1]. The name of the LIM domain is derived from the acronyms of LIN11, ISL1, and MEC3, which are identified from animals containing LIM domain proteins [2,3,4]. The LIM domain is widely distributed and highly conserved in eukaryotes. The universal make-up of the LIM domain comprises two zinc fingers linked together with a short two-amino acid spacer [5]. HaP-LIM1 was first isolated from sunflower (Helianthus annuus L.) pollen [6], and in tobacco (Nicotiana tabacum L.) [7], lily (Lilium longiflorum Thunb L.) [8], Arabidopsis (Arabidopsis thaliana L.) [9], cotton (Gossypium hirsutum L.) [10], tomato (Solanum lycopersicum L.) [11, 12], and foxtail millet (Setaria italica L.) [13], and other species have successively discovered LIM protein
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