Article

The ankyrin repeat gene family in rice: Genome-wide identification, classification and expression profiling

National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, China.
Plant Molecular Biology (Impact Factor: 4.07). 08/2009; 71(3):207-26. DOI: 10.1007/s11103-009-9518-6
Source: PubMed

ABSTRACT Ankyrin repeat (ANK) containing proteins comprise a large protein family. Although many members of this family have been implicated in plant growth, development and signal transduction, only a few ANK genes have been reported in rice. In this study, we analyzed the structures, phylogenetic relationship, genome localizations and expression profiles of 175 ankyrin repeat genes identified in rice (OsANK). Domain composition analysis suggested OsANK proteins can be classified into ten subfamilies. Chromosomal localizations of OsANK genes indicated nine segmental duplication events involving 17 genes and 65 OsANK genes were involved in tandem duplications. The expression profiles of 158 OsANK genes were analyzed in 24 tissues covering the whole life cycle of two rice genotypes, Minghui 63 and Zhenshan 97. Sixteen genes showed preferential expression in given tissues compared to all the other tissues in Minghui 63 and Zhenshan 97. Nine genes were preferentially expressed in stamen of 1 day before flowering, suggesting that these genes may play important roles in pollination and fertilization. Expression data of OsANK genes were also obtained with tissues of seedlings subjected to three phytohormone (NAA, GA3 and KT) and light/dark treatments. Eighteen genes showed differential expression with at least one phytohormone treatment while under light/dark treatments, 13 OsANK genes showed differential expression. Our data provided a very useful reference for cloning and functional analysis of members of this gene family in rice.

Download full-text

Full-text

Available from: Huihui Yu, Aug 28, 2015
0 Followers
 · 
224 Views
  • Source
    • "In higher plants, ANK proteins constitute a large multi-gene family. For example, 175 and 105 ANK repeat genes have been found in rice and the Arabidopsis genome, respectively [12], [13]. However, the function and the underlying mechanism of most of the genes of the ANK family of proteins remains poorly understood. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The ankyrin repeat-containing protein gene OsPIANK1 (AK068021) in rice (Oryza sativa L.) was previously shown to be upregulated following infection with the rice leaf blight pathogen Xanthomonas oryzae pv oryzae (Xoo). In this study, we further characterized the role of OsPIANK1 in basal defense against Magnaporthe oryzae (M.oryzae) by 5' deletion analysis of its promoter and overexpression of the gene. The promoter of OsPIANK1 with 1,985 bps in length was sufficient to induce the OsPIANK1 response to inoculation with M.oryzae and to exogenous application of methyl jasmonate (MeJA) or salicylic acid (SA), but not to exogenous application of abscisic acid (ABA). A TCA-element present in the region between -563 bp and -249 bp may be responsible for the OsPIANK1 response to both M.oryzae infection and exogenous SA application. The JERE box, CGTCA-box, and two MYB binding sites locating in the region between -1985 bp and -907 bp may be responsible for the response of OsPIANK1 to exogenous MeJA. OsPIANK1 expression was upregulated after inoculation with M.oryzae and after treatment with exogenous SA and MeJA. Overexpression of OsPIANK1 enhanced resistance of rice to M.oryzae, although it did not confer complete resistance. The enhanced resistance to M.oryzae was accompanied by enhanced transcriptional expression of SA- and JA-dependent genes such as NH1, WKRY13, PAL, AOS2, PR1b, and PR5. This evidence suggests that OsPIANK1 acted as a positive regulator in rice basal defense mediated by SA- and JA-signaling pathways.
    PLoS ONE 03/2013; 8(3):e59699. DOI:10.1371/journal.pone.0059699 · 3.23 Impact Factor
  • Source
    • "In Oryza sativa, the other ANK C3HC4-type RF proteins have been named XBOS [25]. To date, studies demonstrate that the transcription levels of XB3, XBOS31, XBOS32 and XBOS35 can be regulated by hormones and stress [26], [27]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.
    PLoS ONE 03/2013; 8(3):e58003. DOI:10.1371/journal.pone.0058003 · 3.23 Impact Factor
  • Source
    • "Cock and colleagues previously reported that ANK repeat coding genes are overrepresented in the E. siliculosus genome (Cock et al., 2010), a result which is consistent with what we have found in our studies. The percentage (> 2%) is quite high compared to the other species being studied (Jebanathirajah et al., 2002; Huang et al., 2009; Becerra et al., 2004), where ANK repeat containing proteins generally comprise between 0.4 -0.5% of the total proteins. The presence of ANK repeats within so many proteins (339) in E. siliculosus makes a common function such as an enzymatic activity extremely unlikely and supports the idea that ANK repeats are may be involved in mediating protein–protein interactions (Becerra et al., 2004). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Proteins with Ankyrin repeat motifs (ANK) are found to be associated with diverse biological processes and molecular functions in most of the studied organisms. Several studies have been done on the ANK-motif containing proteins of various model species, but similar studies on their counterparts in brown algae are not available. In this study, we have identified a total of 1,372 ankyrin repeats in 339 proteins of the model brown algae Ectocarpus siliculosus and the consensus sequence of the ANK repeats was determined. The proteins were classified into eight different subfamilies depending on their structural diversity. The data provided in this study may provide useful basis for future reverse genetics analysis of the members of this family.
    Interdisciplinary Sciences Computational Life Sciences 12/2012; 4(4):291-5. DOI:10.1007/s12539-012-0134-9 · 0.66 Impact Factor
Show more