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291533611.Pdf View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Publications of the IAS Fellows Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice Mukesh Jain, Akhilesh K. Tyagi and Jitendra P. Khurana Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, India Keywords Homeobox genes play a critical role in regulating various aspects of plant abiotic stress; homeobox genes; microarray growth and development. In the present study, we identified a total of 107 analysis; reproductive development; rice homeobox genes in the rice genome and grouped them into ten distinct (Oryza sativa) subfamilies based upon their domain composition and phylogenetic analy- Correspondence sis. A significantly large number of homeobox genes are located in the J. P. Khurana, Department of Plant duplicated segments of the rice genome, which suggests that the expansion Molecular Biology, University of Delhi South of homeobox gene family, in large part, might have occurred due to Campus, Benito Juarez Road, New Delhi segmental duplications in rice. Furthermore, microarray analysis was 110021, India performed to elucidate the expression profiles of these genes in different Fax: +91 011 24115270 tissues and during various stages of vegetative and reproductive develop- Tel: +91 011 24115126 ment. Several genes with predominant expression during various stages of E-mail: [email protected] panicle and seed development were identified. At least 37 homeobox genes (Received 6 November 2007, revised 3 were found to be differentially expressed significantly (more than two-fold; March 2008, accepted 31 March 2008) P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and doi:10.1111/j.1742-4658.2008.06424.x abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation. The homeobox genes are key regulators of cell fate the amino acid sequence of HD and the presence of and body plan specification at the early stages of other conserved motifs [4]. The plant homeobox genes embryogenesis in higher organisms. Homeobox genes have been implicated in various developmental pro- contain a conserved 180 bp long DNA sequence cesses and hormone response pathways [4,6,7]. Con- termed a homeobox, which encodes a 60 amino acid vincing evidence is available demonstrating that long DNA-binding domain termed a homeodomain homeobox genes are involved in abiotic and biotic (HD). The HD consists of three a-helices that form a stress responses as well [6,8–12]. The members of class helix-turn-helix DNA-binding motif [1,2]. This motif I KNOTTED1-like homeobox (KNOX) genes are typi- recognizes and binds to specific DNA sequences to cally expressed in shoot apical meristem (SAM) and regulate the expression of target genes. HD-contain- control the balance between meristematic and determi- ing proteins have been identified in diverse organ- nate growth during plant development [13–16]. Loss- isms, such as humans, Drosophila, nematode and of-function mutation in one of the class 1 KNOX plants [3–5]. genes, SHOOT MERISTEMLESS in Arabidopsis and Several homeobox genes have been identified in KNOTTED1 in maize, results in the development of plants and catalogued into different groups, based on embryos lacking SAM [15,17,18]. The WUSCHEL-like Abbreviations BLH, BEL1-like homeobox; DAP, days after pollination; EST, expressed sequence tag; FL-cDNA, full-length cDNA; HD, homeodomain; HD- ZIP, HD-leucine zipper; KNOX, KNOTTED1-like homeobox; MPSS, massively parallel signature sequencing; PHD, plant HD; SAM, shoot apical meristem; UDT1, UNDEVELOPED TAPETUM 1; WOX, WUSCHEL-like homeobox; WUS, WUSCHEL; ZF-HD, zinc finger-HD. FEBS Journal 275 (2008) 2845–2861 ª 2008 The Authors Journal compilation ª 2008 FEBS 2845 Genomic analyses of homeobox genes in rice M. Jain et al. homeobox (WOX) class of genes appears to be essen- domain composition, ORF length, protein length and tial for embryonic patterning [19,20]. The homeobox chromosomal location of each predicted homeobox gene WUSCHEL (WUS) was originally identified as a gene are given in the supplementary Table S1. A central regulator of shoot and floral meristems in Ara- blastp search of these 107 homeobox proteins in the bidopsis [21]. It has been shown that a WUS-like gene annotated proteins of indica rice (cv 93–11) genome is involved in root apical meristem formation in rice revealed that most (at least 100) of these proteins are [22]. BELL-type HD proteins are involved in pattern conserved in both subspecies (data not shown). At formation and development of flowers, fruits and least 72 homeobox proteins predicted from japonica tubers [23–27]. The class III HD-leucine zipper (HD- rice showed ‡ 90% identity over the entire length with ZIP) homeobox genes appear to have a role in shoot the annotated proteins in indica rice. This number may meristem formation, vascular development and estab- increase once a more exhaustive and refined annota- lishing and ⁄ or maintaining abaxial ⁄ adaxial polarity in tion of the indica genome becomes available. leaves and embryo [28–33]. Zinc finger-HD (ZF-HD) The largest number (48) of homeobox proteins were gene family members play overlapping regulatory roles classified into the HD-ZIP family, which was further in floral development in Arabidopsis [34]. subdivided into four distinct subfamilies, termed Although several homeobox genes have been iso- HD-ZIP I (14 members), HD-ZIP II (13 members), lated from rice and a few of them also have been func- HD-ZIP III (nine members) and HD-ZIP IV (12 mem- tionally characterized, a genome-wide analysis has not bers), based on their domain composition and phyloge- been performed so far. In the present study, we identi- netic relationship (Table 1 and Fig. 1). All but one fied 107 homeobox genes in rice, which were classified member of HD-ZIP I and HD-ZIP II subfamilies into ten subfamilies on the basis of their phylogenetic harbor a plant-specific leucine zipper domain, termed relationship and domain composition. Comprehensive the HALZ (homeobox associated leucine zipper) expression analysis shows overlapping and ⁄ or specific domain, which is associated with the homeobox. The expression patterns of these genes in the various rice presence of leucine zipper motif in plant homeobox tissues ⁄ organs and ⁄ or developmental stages analyzed. proteins is markedly different from the case in animal Furthermore, we show that the expression of a large systems in which none of the homeobox genes exam- number of rice homeobox genes is regulated by various ined contain a leucine zipper [37]. Leucine zippers may abiotic stresses. allow the HD-ZIP proteins to interact with each other and other leucine zipper proteins, which may be important for their function. The members of HD-ZIP Results and Discussion III and HD-ZIP IV subfamilies encode an additional domain, termed the START (steroidogenic acute regu- Identification and classification of homeobox latory protein-related lipid-transfer) domain, which is genes in rice a putative lipid-binding domain [38,39]. Recently, a In plants, homeobox genes are represented by a large novel domain, MEKHLA, with significant similarity to multigene family [4,35,36]. In Arabidopsis, approxi- the PAS domain, was identified at the C-terminus of mately 100 homeobox genes were identified and classi- HD-ZIP III proteins [40]. Four rice homeobox fied into several groups based on their domain proteins grouped into the HD-ZIP III subfamily also composition and phylogenetic relationship [4]. In the harbor the MEKHLA domain, which was proposed to present study, the Hidden Markov Model profile and function as a sensory domain [40]. keyword searches followed by domain analysis using The BEL1-like homeobox (BLH) subfamily com- SMART and PFam databases resulted in the identifi- prises 13 homeobox genes, and shows homology to cation of 107 nonredundant potential homeobox pro- Arabidopsis BEL1 protein. These proteins harbor a teins in the rice (Oryza sativa subsp. japonica cv domain of unknown function towards the N-terminal Nipponbare) genome. To examine the evolutionary region of the HD, termed the POX domain, which is relationship among the predicted rice homeobox pro- found exclusively in plant proteins associated with HD teins, a phylogenetic tree was generated from align- [41]. KNOX genes belong to a superfamily TALE ments of their HD sequences by the Neighbour-joining (three amino acid loop extension) because of presence method. This analysis resulted in the formation of ten of an atypical HD, which contains three extra amino distinct clades (Fig. 1). Based on the domain composi- acid stretches between the first and second helices [42]. tion and phylogenetic relationship of their encoded Thirteen rice homeobox proteins belong to the KNOX proteins, the rice homeobox genes were divided into family, which were further divided into two subfami- ten subfamilies (Table 1). The subfamily, tigr locus, lies, KNOX I (nine members) and KNOX II (four 2846 FEBS Journal 275 (2008) 2845–2861 ª 2008 The Authors Journal compilation ª 2008 FEBS M. Jain et al. Genomic analyses of homeobox genes in rice Os03g50920 Os04g35500 Os09g24820 990 Os08g34010 869 Os12g10630 684 770 Os11g13930 Os09g29130 992 Os08g37400 582 Os09g24810 ZF-HD Os12g03110 1000 Os11g03420 Os02g47770 Os05g50310 490
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