Genome-Wide Identification and Expression Analysis of the Tubby-Like Protein Family in the Malus domestica Genome

Abstract

Tubby-like proteins (TLPs), which have a highly conserved β barrel tubby domain, have been found to be associated with some animal-specific characteristics. In the plant kingdom, more than 10 TLP family members were identified in Arabidopsis, rice and maize, and they were found to be involved in responses to stress. The publication of the apple genome makes it feasible to systematically study the TLP family in apple. In this investigation, nine TLP encoding genes (TLPs for short) were identified. When combined with the TLPs from other plant species, the TLPs were divided into three groups (group A, B, and C). Most plant TLP members in group A contained an additional F-box domain at the N-terminus. However, no common domain was identified other than tubby domain either in group B or in group C. An analysis of the tubby domains of MdTLPs identified three types of conserved motifs. Motif 1 and 2, the signature motifs in the confirmed TLPs, were always present in MdTLPs, while motif 3 was absent from group B. Homology modeling indicated that the tubby domain of most MdTLPs had a closed β barrel, as in animal tubby domains. Expression profiling revealed that the MdTLP genes were expressed in multiple organs and were abundant in roots, stems, and leaves but low in flowers. An analysis of cis-acting elements showed that elements related to the stress response were prevalent in the promoter sequences of MdTLPs. Expression profiling by qRT-PCR indicated that almost all MdTLPs were up-regulated at some extent under abiotic stress, exogenous ABA and H2O2 treatments in leaves and roots, though different MdTLP members exhibited differently in leaves and roots. The results and information above may provide a basis for further investigation of TLP function in plants.

Comprehensive Profiling of Tubby-Like Protein Expression Uncovers Ripening-Related TLP Genes in Tomato (Solanum lycopersicum)

“…Based on the analysis of the typical domains and gene structure of TLPs, we found that all TLPs expect TLP11 contain both the Tub domain and F-box domain, which is consistent with previous reports that most plant TLPs contain the F-box domain [2,4,6,7]. Moreover, we found that the motifs in TLP2 are different from other TLPs (Figure 2).…”

“…Specifically, most TLP promoters contained both CGTCA-motif and TGACG-motif which were related to the jasmonate acid response. Moreover, ARE, which was related to anaerobic reaction and ABRE, which was associated to the abscisic acid response, were found in most TLPs' promoters [2,4,6,15]. These results suggest that TLPs may play an important role in stress response, but this needs further experimental verification.…”

“…Tubby-like proteins (TLPs) have been identified in both animals and plants [15]. In several plant species, TLP family genes were identified and mainly shown to be involved in stress response [2,4,6,7]. However, to date, the TLP family in tomato, one of the most important model plants for fruit ripening research, had not been identified.…”

“…TLPs are characterized by a signature of the C-terminal tubby domain that forms a closed β barrel with 12 anti-parallel strands and a central hydrophobic α helix [3]. In plants, most known TLPs contain not only a conserved C-terminal tubby domain but also a highly conserved F-box domain at their N-terminus, which is different from the high divergence of the N-terminal sequence in animals [4][5][6][7][8].…”

Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis of MdPIF4 in Malus domestica

“…Apple ( Malus domestica ) is an important commercial fruit crop, and its production is highly affected by environmental factors, especially light [ 29 , 30 ]. PIFs play a central role in adapting plants to different light conditions; however, identification and functional analysis of PIFs in apples have not been systematically investigated, except MdPIF1 [ 31 ].…”